TY  - GEN
N2  - In eukaryotic cells, DNA transcription, replication and repair events are controlled by the regulation of DNA compaction mechanisms that determine the open and closed chromatin states. Nucleosomes are the basic DNA packaging units of chromatin. The nucleosome core (NC) consists of a core histone protein octamer with approximately two tight superhelical turns of DNA wrapped around it. The NC is extended at its entry and exit points by linker DNA (L-DNA) and a linker histone (LH) protein binds between the two L-DNA arms to form a chromatosome. The dyad is the single DNA base pair between the nucleosome entry and exit points determining the symmetry axis and is used to define the position of LH binding to a nucleosome. For LH - nucleosome binding, previous studies indicate both on- and off-dyad binding modes, as well as different LH orientations. Thus, the molecular determinants of the structure of LH ? nucleosome complex and the dynamics of LH ? nucleosome binding are not fully understood.
The aim of the research described here was to obtain an atomic-detail level understanding of chromatosome formation. Analysis of the experimentally determined structures of LH ? nucleosome complexes showed that instead of a single 3D structure, an ensemble of structures of LH ? nucleosome complexes exists. To understand the distribution of these ensembles, normal mode analysis (NMA), standard and accelerated molecular dynamics (MD & AMD) and Brownian dynamics (BD) simulations were applied to LH, nucleosome and chromatosome systems. MD and AMD simulations showed that the globular domain of the LH (LH GD) prefers to be in its closed form in solution. Upon nucleosome binding, the LH GD structure transformed to an open structure due to hydrophobic interactions with the L-DNA of the nucleosome. Additionally, LH GD binding constrained the flexibility of the L-DNA and affected the directions of movement of the L-DNA arms. BD simulations indicated that various chromatosome configurations were possible depending on LH GD sequence and L-DNA opening angles. These findings suggest that LH ? nucleosome binding is mediated by a combination of conformational selection and induced fit mechanisms.
Further BD simulations show that chromatosome configurations were affected by single point mutations in the LH GD and varied for different LH isoforms. My results indicate that by making specific single point mutation exchanges, it is possible to swap LH ? nucleosome configurations among different LH GD isoforms. Similar shifts were observed in chromatosome configuration upon introduction of post translational modifications (PTMs) in the LH GD.
I applied BD simulations to compute dissociation rate constant (koff) values and compare them with previously reported fluorescence recovery after photobleaching (FRAP) data on the binding of various LH mutants to chromatin. The results of the BD simulations correspond with the relative trends in measured FRAP recovery half-times (t50) of LH ? chromatin binding of various LH
mutants. The results thus enable the interpretation of the FRAP data in terms of a physical model of LH ? nucleosome binding.
My thesis provides detailed insights into the structure, dynamics and kinetics of chromatosome formation in eukaryotes. The results presented in this work can guide further experiments on the sequence determinants of LH ? nucleosome binding.
A1  - Öztürk, Mehmet Ali
AV  - public
TI  - A computational approach to decipher chromatosome
structure determinants
Y1  - 2019///
ID  - heidok25231
CY  - Heidelberg
UR  - https://archiv.ub.uni-heidelberg.de/volltextserver/25231/
ER  -