Fig. 5: MV-NLP can form nucleosome stacks in silico.
Two parameters were measured to assess the stability of di-nucleosome stacks: The mean variation of (A, C) the root mean square deviation (r.m.s.d) of the overall structure compared to the start of the simulation, and (B, D) the distances between the center of gravity of the two nucleosomes over the simulation time are plotted for the human telomeric di-nucleosome (green), MV-NLP (blue), MV-varNLP (brown), MV-hybridNLP (purple) and a control for MV-varNLP wherein inter-nucleosomal protein-protein contacts were mutated in silico to Glu (grey). C, D show a simulation of di-nucleosomes where 10 bp at the DNA linker portion connecting both nucleosomes were removed to sever the connection between the two particles. The larger r.m.s.d variations at the beginning of the simulation for the human telomeric di-nucleosome are due to the long tails that collapse onto the DNA, as previously observed for eukaryotic mono-nucleosomes21. The lighter area around the mean curve corresponds to the standard variation around the mean curve, from three replicates. Individual tracks are found in Supplementary Fig. 7.
