Conformations of Nucleosome Arrays in Solution
from Small-Angle Scattering
Steven C.
†*
Howell,
Xiangyun
Background
*
Qiu,
Joseph E.
†
Curtis,
Small-Angle Scattering
†NIST
Center for Neutron Research, Gaithersburg MD
*Department of Physics, The George Washington University, Washington DC
CG—MC Model for dsDNA
Chromatin is highly packaged DNA.
CG Modeling of 4x167 Array
All
DNA in your cells:
• 6x109 base pairs
• ~2 m stacked end-to-end
Best
http://micro.magnet.fsu.edu/cells/nucleus/image
s/chromatinstructurefigure1.jpg}
DNA in your body:
• ~100 x 109 km
• ~670 x distance to the sun
Momentum Transfer:
Wormlike Bead—Rod Model: (Dorfman group, U. of Minnesota)
Scattering Intensity:
Low Concentration Scattering Intensity:
Packaging purposes:
• Organized compaction
• Protection
• Regulation
Pair-Distance Distribution:
Chromatin structure impacts genetic processes.
Harmonic Twist Energy: (Olson, Rutgers U. & Zhurkin, NIH)
• Expression
• Replication
• Repair
4x167 Nucleosome Array
Duhl et al. Nature Genetics, 1994;
DOI: 10.1038/ng0994-59
Packaging of nucleosomes is not well understood.
• DNA structure Solved
(Watson, Crick, Wilkins, and Franklin)
• Nucleosome Crystal Structure Solved
(Luger, Richmond, et al. PDB ID: 1KX5)
• Some Success in Crystallizing Nucleosome Arrays
(Schalch, Richmond, et al. PDB ID: 1ZBB)
SAS data from 4x167
nucleosome arrays with
and without the gH5
linker histone protein in
low (10 mM K+) and
high (additional 1 mM
Mg2+) ionic screening.
Ion Screening Effect:
• Peak shifts from 0.040
Å-1 in K+ to 0.018 Å-1 in
Mg2+.
• Multi-domain structure
in K+ becomes singledomain in Mg2+.
Representation of PDB ID: 1KX5
gH5 Linker Effect:
• Significant
structure
change from high ionic
screening.
• Negligible
structure
change from low ionic
screening.
Representation of PDB ID: 1ZBB
How does the solution structure
compare with the crystal structure?
gH5 in 1 mM
Mg2+
matches
1ZBB best.
Conclusions
• Measured nucleosome arrays using SAS at low and high
ionic screening
• 4x167 (shown)
• 1x147
• 4x167 gH5 (shown)
• 2x167
• 12x167
• 3x167
• Developed a CG simulation algorithm for dsDNA
• Metropolis MC sampling of dsDNA as a Markov Chain
• Reproduces dsDNA bend and twist energetics
• Generates robust atomic models
• Filtered ensembles 4x167 nucleosome array models against
SAS data
• Identified specific differences between the 1ZBB crystal and
1mM Mg2+ solution ensemble
This research was supported by:
• Cornell High Energy Synchrotron Source, NSF DMR-1332208
• National Synchrotron Light Source, DOE DE-AC02-98CH10886
• CCP-SAS, EPSRC EP/K039121/1 and NSF CHE-1265821
Presented at the 4th CCP-SAS Workshop, 23 May 2016