Modeling and small-angle neutron scattering spectra of chromatin supernucleosomal structures at genome scale. Ilatovskiy, A., Lebedev, D., Filatov, M., Grigoriev, M., Petukhov, M., & Isaev-Ivanov, V. Journal of Applied Physics, 2011. cited By 1![Modeling and small-angle neutron scattering spectra of chromatin supernucleosomal structures at genome scale [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex Eukaryotic genome is a highly compacted nucleoprotein complex organized in a hierarchical structure based on nucleosomes. Detailed organization of this structure remains unknown. In the present work we developed algorithms for geometry modeling of the supernucleosomal chromatin structure and for computing distance distribution functions and small-angle neutron scattering (SANS) spectra of the genome-scale (∼106 nucleosomes) chromatin structure at residue resolution. Our physical nucleosome model was based on the mononucleosome crystal structure. A nucleosome was assumed to be rigid within a local coordinate system. Interface parameters between nucleosomes can be set for each nucleosome independently. Pair distance distributions were computed with Monte Carlo simulation. SANS spectra were calculated with Fourier transformation of weighted distance distribution; the concentration of heavy water in solvent and probability of H/D exchange were taken into account. Two main modes of supernucleosomal structure generation were used. In a free generation mode all interface parameters were chosen randomly, whereas nucleosome self-intersections were not allowed. The second generation mode (generation in volume) enabled spherical or cubical wall restrictions. It was shown that calculated SANS spectra for a number of our models were in general agreement with available experimental data. © 2011 American Institute of Physics.
@ARTICLE{Ilatovskiy2011,
author={Ilatovskiy, A.V. and Lebedev, D.V. and Filatov, M.V. and Grigoriev, M. and Petukhov, M.G. and Isaev-Ivanov, V.V.},
title={Modeling and small-angle neutron scattering spectra of chromatin supernucleosomal structures at genome scale},
journal={Journal of Applied Physics},
year={2011},
volume={110},
number={10},
doi={10.1063/1.3661987},
art_number={102217},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-82555167434&doi=10.1063%2f1.3661987&partnerID=40&md5=8a4868aeeffdd6637dac55d1e4fa84a9},
affiliation={Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, Russian Federation; Research and Education Center Biophysics, PNPI RAS, St. Petersburg State Polytechnical University, St. Petersburg, Russian Federation; Laboratoire Biologie Moléculaire Eukaryote, CNRS-Université Paul-Sabathier, Toulouse, France},
abstract={Eukaryotic genome is a highly compacted nucleoprotein complex organized in a hierarchical structure based on nucleosomes. Detailed organization of this structure remains unknown. In the present work we developed algorithms for geometry modeling of the supernucleosomal chromatin structure and for computing distance distribution functions and small-angle neutron scattering (SANS) spectra of the genome-scale (∼106 nucleosomes) chromatin structure at residue resolution. Our physical nucleosome model was based on the mononucleosome crystal structure. A nucleosome was assumed to be rigid within a local coordinate system. Interface parameters between nucleosomes can be set for each nucleosome independently. Pair distance distributions were computed with Monte Carlo simulation. SANS spectra were calculated with Fourier transformation of weighted distance distribution; the concentration of heavy water in solvent and probability of H/D exchange were taken into account. Two main modes of supernucleosomal structure generation were used. In a free generation mode all interface parameters were chosen randomly, whereas nucleosome self-intersections were not allowed. The second generation mode (generation in volume) enabled spherical or cubical wall restrictions. It was shown that calculated SANS spectra for a number of our models were in general agreement with available experimental data. © 2011 American Institute of Physics.},
correspondence_address1={Ilatovskiy, A.V.; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, Russian Federation; email: andreyi@omrb.pnpi.spb.ru},
issn={00218979},
coden={JAPIA},
language={English},
abbrev_source_title={J Appl Phys},
document_type={Conference Paper},
source={Scopus},
}
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