view article
Figure 3
Simulating the breathing behaviour of CPD phosphodiester or formacetal linkage-containing dsDNA–MmCPDII complexes. (a) DNA kink-angle population analysis, with the middle of the distribution highlighted by a dotted line and value in the corresponding colour. The bins corresponding to either the PDM (PDB entry 5zcw, complex I) or FDM (PDB entry 2xrz, complex II) crystal structures are highlighted with green and blue asterisks, respectively. Top, populations for CPD phosphodiester-containing simulations (simulation 1 in black, simulation 2 in red). Bottom, populations for two of the CPD formacetal-containing simulations (simulation 3 in black, simulation 4 in red). (b) Non-occluded and total volume population analysis for the unpaired DNA bubble. Non-occluded volumes (i.e. the volume not covered by the amino acids occluding the unpaired space) are always smaller and on the left side of the graph. The total volume is always larger and on the right side of the graph. The middle point of the distribution is highlighted via a dotted line and the corresponding value. Top, populations for the two phosphodiester-containing simulations (simulations 1 and 2 in black and red, respectively). Bottom, populations for two of the formacetal-containing simulations (simulations 3 and 4 in black and red, respectively). (c) Water-density analysis for the phosphodiester- and formacetal-containing systems. Left, overall representation of the water-density analysis system. An analysis box (black lines) was drawn roughly around the area of interest, comprising the unpaired bubble and portions of the surrounding solvent. The box was divided into voxels of 0.5 × 0.5 × 0.5 Å. Here, red objects show regions of the analysis box containing waters with an occupancy higher than 5 in simulation 1 (containing phosphodiester) and pale blue objects those in simulation 3 (containing formacetal). Right, highest water occupancy y-axis slice at the 12th y voxel (dotted plane on the left panel), shown for each of the simulations. High-occupancy voxels are shown in red and voxels with solvent-equivalent densities are shown in blue. Voxels occupied by solute, i.e. with water densities below 1, are shown in green. For orientation purposes, the approximate positions of dC6, dC9, C0, P0 and Arg429 are shown on the map, although they are not necessarily coplanar with the 12th y voxel.

IUCrJ
Volume 5| Part 5| September 2018| Pages 608-618
ISSN: 2052-2525
https://doi.org/10.1107/S205225251800996X