Fig. 3: PPIA interacts with intrinsically disordered proteins.
a, 3D models of the wild-type (WT) PPIA structure and the G104A mutant PPIA, which has restricted access to the catalytic core17,32. Dashed white lines outline the PPIA catalytic core. The arrow indicates the additional A104 methyl group in the mutant (light blue spheres). The PPIA structure was sourced from X-ray crystallography data deposited at the Protein Data Bank (7ABT)11. b, Expression pattern of WT and mutant PPIA proteins. 293T cells were transiently transfected with WT PPIA-GFP, PPIA (G104A)-GFP mutant or PPIA (H92Y)-GFP catalytic core mutant. At 24 h post transfection, the expression pattern of the WT and PPIA mutant proteins was assessed with a Zeiss Celldiscoverer 7 imaging system, using a GFP filter (bottom) or bright field (top). Scale bars, 20 µm. Data are representative of three independent experiments. c, Left: Immunoprecipitation and SYPRO Ruby gel stain of triple FLAG-tagged wild-type (3XF-WT PPIA) and G104A point-mutant PPIA (3XF-Mutant PPIA) were performed in 293T cells to identify PPIA-interacting proteins. The grey arrow indicates positive enrichment for PPIA protein in the pull-down fractions. Right: purity of the cytosolic cell lysates was verified by a lack of histone H3 protein expression in this subcellular fraction. Data are representative of three independent experiments. d, Gene Ontology enrichment analysis of 3XF-WT PPIA versus 3XF-Mutant PPIA immunoprecipitation–MS results. Data represent 385 consistently identified proteins in 293T cells (overlapping MS results from two separate experiments are depicted). e, Quantification of the fraction of IDRs in the total proteome versus 3XF-WT PPIA-interacting proteins. **P < 0.01; two-sided Wilcoxon rank-sum test (violin plot lines indicate quartiles; n = 385 PPIA target proteins). GFP, green fluorescent protein.
