Impact of pH on fuzzy interactions between two intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) and their regions (IDRs) play crucial roles in cellular functions despite their lack of stable three-dimensional structures. In this study, we investigate the interactions between the C-terminal domain of protein 4.1G (4.1G CTD) and the nuclear mitotic apparatus protein (NuMA) under varying pH and salt ion conditions to understand the regulatory mechanisms affecting their binding. 4.1G CTD and NuMA bind effectively under neutral and alkaline conditions, but their interaction is disrupted under acidic conditions (pH 3.6). The protonation of positively charged residues at the C-terminal of 4.1G CTD under acidic conditions leads to increased electrostatic repulsion, weakening the overall binding free energy. Secondary structure analysis shows that specific regions of 4.1G CTD remain stable under both pH conditions, but the C-terminal region (aa 990−1000) and the N-terminal region of NuMA (aa 1800−1810) exhibit significant reductions in secondary structure probability under acidic conditions. Contact map analysis and solvent-accessible surface area analysis further support these findings by showing a reduced contact probability between these regions under pH 3.6. These results provide a comprehensive understanding of how pH and ionic strength regulate the binding dynamics of 4.1G CTD and NuMA, emphasizing the regulatory role of electrostatic interactions.