Analysis of H-SASA profiles dependence of various parameters.
DNA cleavage by hydroxyl-radicals is accomplished through abstraction of deoxyribose hydrogen atoms. Hence their solvent accessible surface area (H-SASA) can be used as a proxy to estimate the probability of cleavage given a PDB structure.
However, H-SASA depends on a number of parameters (structure quality and conformation, probe radius, choice of atomic radii set). Below we provide an analysis of the influence of these parameters on the H-SASA profiles in nucleosome.
Structure choice
Structures with hydrogen atoms added in a variety of ways were considered:
- scCSE4_601TA_nucl_H_Ndist.pdb was generated by REDUCE program as provided in AmberTools17 with following command:
reduce -NUClear scCSE4_601TA_nucl.pdb > scCSE4_601TA_nucl_H_Ndist.pdb
The -NUClear option instucts to use nuclear X-H distances (~1.09 A for sugars) rather than default electron cloud distances (~0.97A).
- scCSE4_601TA_nucl_H_ELdist.pdb was generated by REDUCE program as provided in AmberTools17 with following command:
reduce scCSE4_601TA_nucl.pdb > scCSE4_601TA_nucl_H_Ndist.pdb
The default electron cloud distances of ~0.97A for X-H bonds in sugars are used.
- scCSE4_601TA_nucl_H_MD1ns.pdb generated by VMD psfgen command with CHARMM36 force field and then simulated using molecular dynamics simulations for 1 ns in explicit solvent using NAMD.
- scCSE4_601TA_nucl_H_MD2ns.pdb - previous structure after simulations for 2 nanoseconds.
- ../exampleMD - provides 50 frames from a molecular dyanmics trajectory, which are used to calculate averaged profiles.
Calculating H-SASA profiles with different parameters.
- H-SASA_params_scan.py implements calculation of H-SASA profiles for the above listed structures with a number of different parameters by varying atomic van-der-Waals radii sets (default in FreeSASA, AMBER12 force field, CHARMM36 force field), probe radius used to build the surface (from 1 A to 5 A). SASA values for the following atoms are calculated separately allowing to assess their contributions: H1’, H2’+H2’’, H3’, H4’, H5’+H5’’.
Analysis of the results