Supplementary Figure 5: Comparison between theoretically estimated DNA cleavage profiles generated from X-ray-derived structure and MD simulations. | Nature Protocols

Supplementary Figure 5: Comparison between theoretically estimated DNA cleavage profiles generated from X-ray-derived structure and MD simulations.

From: Structural interpretation of DNA–protein hydroxyl-radical footprinting experiments with high resolution using HYDROID

Supplementary Figure 5

Theoretically estimated DNA cleavage profiles (H-SASA profiles) for S. cerevisiae centromeric nucleosome reconstituted on 601TA sequence based on all deoxyribose hydrogen atoms were obtained for two cases: from an X-ray-derived homology model (DNA geometry strictly corresponds to the X-ray structure) and averaged over frames of MD simulation. Differences are attributed to the relaxation of small DNA structure irregularities and averaging over DNA backbone dynamics.

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