Fig. 7: Formation/relaxation of twist-defects in NCPtt145 simulation.
From: Histone dynamics mediate DNA unwrapping and sliding in nucleosomes
a Plots of DNA relative twist profile along the DNA. The DNA sequence for the top strand of NCPtt145 is given along the X-axis. b A heatplot of changes in nucleotide positions for the proximal half of the top DNA strand during simulations. Starting from ~4 µs the half twist-defect relaxation causes the shift on the top DNA strand nucleotides in the region ~−50 to −72 by one step toward the dyad. c–e Successive stages of twist-defect relaxation at SHL -5 resulting in DNA sliding by 1 bp from SHL −7 to SHL −5. Snapshots are overlaid on the X-ray structure shown in cyan. Three base pairs (positions −59, −54, −49, and −44) around the SHL −5 region are highlighted in orange (X-ray positions) and magenta (MD positions). L1L2 binding sites are the DNA binding sites formed by L1 and L2 loops of histone folds. SHL stands for superhelix location.
