Extended Data Fig. 9: Influence of H2BK34ub modification on nucleosome structure and Dot1L stability by Molecular Dynamics.
From: H2B Lys34 Ubiquitination Induces Nucleosome Distortion to Stimulate Dot1L Activity
a, RMSD of DNA GCT (−49~−47) motif from MD simulation models. The unmodified-nucleosome model was depicted as orange, and H2BK34ub-nucleosome model was depicted as blue. b, Distance changes of DT143-H3T45 over MD simulation time, unmodified-nucleosome model was colored as orange, and H2BK34ub-nucleosome was colored as blue. c, Distance representation of DT143-H3T45. DT143-H3T45 from the cryo-EM structure of unmodified nucleosome and the frame of H2BK34ub-nucleosome model at 400 ns were shown. d, Conformations of histones during MD simulations. e, Alignments of H3 and H4 histones. f, Interaction snapshot between H4 N-terminus and Dot1L. g, RMSD changes of Dot1L in Dot1L-H2BK34ub complex model over MD simulation time. h, RMS fluctuation (RMSF) of each Dot1L residue in Dot1L-H2BK34ub complex model over MD simulations. i, Dot1L stability representation relevant to h. Dot1L with larger fluctuation was in blue, and the relatively stable Dot1L was in orange.
