Figure 1.

The nucleosome and its acidic patch. (a) Electrostatic potential view of the nucleosome surface. The electrostatic rendering was performed using APBS tools in PyMOL (http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol#TOC-Generating-the-PQR). A pqr file was generated from the 1KX5 histone octamer (no DNA), using pdb2pqr software. APBS was then run through PyMOL. The electrostatic potential displayed is between −25 (red) and +25 (blue) kT e^–1. (b) Close-up view of the acidic patch. Histone H2A is shown in yellow and H2B in red. The α1- and αC-helices of H2B, α2- and αC-helices of H2A and the eight residues that make up the acidic patch are labelled. PDB 1KX5.