Fig. 3: Citrullination impacts protein dynamics by promoting the destabilization of protein folding. | Nature Communications

Fig. 3: Citrullination impacts protein dynamics by promoting the destabilization of protein folding.

From: Citrullination modulates antigen processing and presentation by revealing cryptic epitopes in rheumatoid arthritis

Fig. 3

a PyMOL structural alignment of native (gray) and PAD2/4-combined citrullinated (colored by antigen) PDB structures predicted by AlphaFold AI system, excluding fibrinogen α chain due to computational constraints. Mass spectrometry-confirmed citrullination sites from PAD2 and PAD4 combined are denoted as purple spheres on the citrullinated structure. b Predicted PAD2-citrullinated structures with significantly changed regions color-coded according to legend and PAD2 citrullination sites denoted as purple spheres. See Supplementary Fig. 4 for PAD4-citrullinated structures. c Violin plots depicting the actual minus expected distance from each significantly changed region to the nearest citrulline residue in the 3-dimensional structure. d, e Antigen processing change score versus RMSD value or 1/TM-score, respectively, analyzed by simple linear regression for PAD2- or PAD4-citrullinated (cit) vimentin, fibrinogen β, and hnRNP A2/B1.

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