Fig. 8: Molecular dynamics (MD) simulations using Xplor-NIH on mouse RIPK3 fibrils and a hetero-amyloid model of mouse RIPK1/RIPK3.
From: The amyloid structure of mouse RIPK3 (receptor interacting protein kinase 3) in cell necroptosis
a The best four structures of mouse RIPK3 fibril after 50 ps MD, showing the fibril developing a left-hand twist. b The structure alignment of RIPK3 conserved tetrad sequence from human RIPK1/RIPK3 hetero-amyloid structure (purple, 5v7z.pdb), mouse RIPK3 fibril structure (blue, 6JPD.pdb) and mouse RIPK3 fibril after 50 ps MD from (a) (cyan). c The best four structures of mouse RIPK1/RIPK3 hetero-amyloid after 50 ps MD run, showing the opening the β-arches formed by the 1st and 2nd β-strand. The mouse RIPK3 fibril structure was adopted as the starting configuration for the MD. The sequence alignment for mouse RIPK1 and RIPK3 is shown on the top. d The structure comparison between c (cyan, showing only the best two structures for clarity, residue V448, I450 was also shown in one subunit) and RIPK1/RIPK3 from the human RIPK1/RIPK3 hetero-amyloid structure (purple, 5v7z.pdb). e The proposed mechanism showing RIPK3 structural transformation from initial RIPK1–RIPK3 binding to RIPK3 fibril formation.
