Abstract
This paper uses atomistic molecular mechanics within the framework of the JUMNA model to study the bending properties of DNA segments, with emphasis on understanding the role of the 10 bp periodicity associated with AA repeats that has been found to dominate in nucleosomal DNA. The calculations impose a bending potential on 18 bp segments that is consistent with nucleosome structures (i.e., radius of curvature of 4.1 nm), and then determine the energies of the minimum energy structures for different values of the rotational register (a measure of the direction of bending of the DNA) subject to forces derived from the Amber force field (parm99bsc0). The results show that sequences that contain the 10 bp repeats but are otherwise random have a narrow distribution of rotational register values that minimize the energy such that it is possible to combine several minimized structures to give the 147 bp nearly planar loop structure of the nucleosome. The rotational register values that lead to minimum bending energy with 10 bp AA repeats have a narrower minor groove, which points toward the histone interior at the positions of the AA repeats, which is a result that matches the experiments. The calculations also show that these sequences have a relatively flat potential energy landscape for bending to a 4.1 nm radius of curvature. Random sequences that do not have the 10 bp AA repeats have less stable bent structures, and a flat rotational register distribution, such that low energy nearly planar loops are less likely.
| Original language | English |
|---|---|
| Pages (from-to) | 8638-8644 |
| Number of pages | 7 |
| Journal | Journal of Physical Chemistry B |
| Volume | 115 |
| Issue number | 26 |
| DOIs | |
| Publication status | Published - Jul 7 2011 |
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ASJC Scopus subject areas
- Physical and Theoretical Chemistry
- Materials Chemistry
- Surfaces, Coatings and Films
Cite this
Modeling DNA-bending in the nucleosome : Role of AA periodicity. / Prytkova, Tatiana R.; Zhu, Xiao; Widom, Jonathan; Schatz, George C.
In: Journal of Physical Chemistry B, Vol. 115, No. 26, 07.07.2011, p. 8638-8644.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Modeling DNA-bending in the nucleosome
T2 - Role of AA periodicity
AU - Prytkova, Tatiana R.
AU - Zhu, Xiao
AU - Widom, Jonathan
AU - Schatz, George C
PY - 2011/7/7
Y1 - 2011/7/7
N2 - This paper uses atomistic molecular mechanics within the framework of the JUMNA model to study the bending properties of DNA segments, with emphasis on understanding the role of the 10 bp periodicity associated with AA repeats that has been found to dominate in nucleosomal DNA. The calculations impose a bending potential on 18 bp segments that is consistent with nucleosome structures (i.e., radius of curvature of 4.1 nm), and then determine the energies of the minimum energy structures for different values of the rotational register (a measure of the direction of bending of the DNA) subject to forces derived from the Amber force field (parm99bsc0). The results show that sequences that contain the 10 bp repeats but are otherwise random have a narrow distribution of rotational register values that minimize the energy such that it is possible to combine several minimized structures to give the 147 bp nearly planar loop structure of the nucleosome. The rotational register values that lead to minimum bending energy with 10 bp AA repeats have a narrower minor groove, which points toward the histone interior at the positions of the AA repeats, which is a result that matches the experiments. The calculations also show that these sequences have a relatively flat potential energy landscape for bending to a 4.1 nm radius of curvature. Random sequences that do not have the 10 bp AA repeats have less stable bent structures, and a flat rotational register distribution, such that low energy nearly planar loops are less likely.
AB - This paper uses atomistic molecular mechanics within the framework of the JUMNA model to study the bending properties of DNA segments, with emphasis on understanding the role of the 10 bp periodicity associated with AA repeats that has been found to dominate in nucleosomal DNA. The calculations impose a bending potential on 18 bp segments that is consistent with nucleosome structures (i.e., radius of curvature of 4.1 nm), and then determine the energies of the minimum energy structures for different values of the rotational register (a measure of the direction of bending of the DNA) subject to forces derived from the Amber force field (parm99bsc0). The results show that sequences that contain the 10 bp repeats but are otherwise random have a narrow distribution of rotational register values that minimize the energy such that it is possible to combine several minimized structures to give the 147 bp nearly planar loop structure of the nucleosome. The rotational register values that lead to minimum bending energy with 10 bp AA repeats have a narrower minor groove, which points toward the histone interior at the positions of the AA repeats, which is a result that matches the experiments. The calculations also show that these sequences have a relatively flat potential energy landscape for bending to a 4.1 nm radius of curvature. Random sequences that do not have the 10 bp AA repeats have less stable bent structures, and a flat rotational register distribution, such that low energy nearly planar loops are less likely.
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U2 - 10.1021/jp203564q
DO - 10.1021/jp203564q
M3 - Article
VL - 115
SP - 8638
EP - 8644
JO - Journal of Physical Chemistry B
JF - Journal of Physical Chemistry B
SN - 1520-6106
IS - 26
ER -