A cryo EM fiber structure.
In all cases, we are finding that nucleosomes that have the largest overlap between them tend to be in contact via the H4-acidic patch interaction.
Unlike the crystal structures, where this tends to be obvious for high overlaps, the cryo-EM structure doesn't show this as clearly, and the simulations
tend to be more ambiguous. The heatmap below shows the average (x,y) coordinate of interaction on the top face of a nucleosome, with the centers of the
core histones plotted on top of it. Note the region of most interaction is between H4 and the acidic patch, which is remarkable given the flexibility
allotted to the simulations.
The regions of contact on the top face of the nucleosomes in the simulations. Note that the region is between the acidic patch (AP)
and H4.
Week 9:
This week I have been working on my final technical report as well as code documentation so that others can use the software
I developed. Thanks to everyone who made this a great REU!
Presentations
References
- Lu et al. Structure and Conformation of Helical Nucleic Acids:
Analysis Program (SCHNAaP). J. Mol Bio (1997) 273, 668-680.