Chapter 4 │ Page 134 Table 4. Binding persistence (i.e. percentage of time that the N-O distances are below 4.5 Å) of the salt bridges that play an important role in the ligand-receptor complex systems, during the last 100 ns of the three replicate simulations. The salt bridges that are present in the crystal structure of the complexes are written in italic. the stronger Glu187KIR2DL1 – Lys80HLA-Cw4 interaction and weaker Asp135KIR2DL1 – Arg145HLA-Cw4/ Asp183KIR2DL1 – Lys146HLA-Cw4 interaction) however seem to cancel out, as we observed no significant e ect of the investigated oxidations on the binding free energy. In addition to the salt bridges Salt bridge binding HLA-E CD94 Native Oxidized Arg68 Glu164 29% 20% Arg68 Asp168 51% 30% Asp69 Arg171 26% 20% Arg75 Asp163 1% 4% Arg75 Glu164 9% 4% Arg79 Asp163 26% 19% HLA-E NKG2A Asp149 Arg137 8% 5% Glu154 Arg137 6% 7% Glu161 Lys217 28% 8% Asp162 Lys199 37% 47% Asp162 Arg215 17% 6% Asp162 Lys217 15% 20% Glu166 Lys199 4% 34% Salt bridge binding HLA-Cw4 KIR2DL1 Native Oxidized Arg69 Glu21 12% 0% Lys80 Asp183 42% 25% Lys80 Glu187 47% 68% Arg145 Asp135 18% 5% Lys146 Asp135 0% 31% Lys146 Asp183 90% 2% Lys146 Glu187 15% 10% Lys8 (peptide) Glu187 30% 30%
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