Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions
Fig 2
Comparison of local binding contributions between conditions and PTM types for the interface-located PTMs.
ΔΔGbind,contribution values in two conditions for each type of PTM (acetylation in blue, phosphorylation in orange), where NC stands for “normal conditions” and SC for “stress conditions”. Acetylation more frequently contributes to binding in a stabilizing way, as reflected in the majority of the violin plot being below zero, while the opposite is true for phosphorylation. No significant differences were found between ΔΔGbind,contribution for PTMs of the same type between normal and stress conditions (p-values indicated on the plots). Comparison of ΔΔGbind,contribution values between different types of PTMs within a given condition shows several statistically significant differences, connected by the lines (full line for NC and dashed for SC) and marked with stars above the plots. The corresponding p-values are: p(Lys-Ser, NC) = 1.3e-76, p(Lys-Thr, NC) = 7.7e-39, p(Lys-Tyr, NC) = 2.3e-03, p(Ser-Thr, NC) = 2.0e-02, and p(Ser-Thr, SC) = 2.9e-02. Cohen’s d-values indicate that the effect sizes vary from small (d(Ser-Thr, SC) = 0.29, d(Ser-Thr, NC) = 0.45) to large (d(Lys-Ser, NC) = 1.43, d(Lys-Thr, NC) = 1.82, d(Lys-Tyr, NC) = 2.23).