Eukaryotic genomes are packaged into chromatin through association with small positively charged histone proteins, which can fold further to form higher-order structures. In vivo, numerous proteins are involved in the regulation of chromatin assembly and folding. Mis-regulation may lead to cancer. However, structural mechanisms of chromatin assembly, folding and their regulation remain largely unknown. For the last several years, my research group have combined solution NMR and X-ray crystallography to study the structures of protein-protein and protein-DNA complexes that relate to these issues. Major results from our study and future perspectives will be presented.

Related publications:

• Zhou et al. Structural basis for recognition of centromere histone variant CenH3 by the chaperone Scm3. Nature 472, 234-237 (2011).
• Kato et al. Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR. Proc Natl Acad Sci 108, 12283-12288 (2011).
• Kato et al. A conserved mechanism for centromeric nucleosome recognition by centromere protein CENP-C. Science, 340, 1110-1113 (2013).
• Zhou et al. Structural insights into the histone H1-nucleosome complex. Proc Natl Acad Sci 110, 19390-19395 (2013).
• Zhou et al. Structural Mechanisms of Nucleosome Recognition by Linker Histones. Mol Cell 58, 628-638 (2015).

The frequency-dependent dielectric response of DNA in solution probes the dynamics of the nucleic acid polymer and its counter-ion atmosphere on time scales important for cellular processes. The dielectric response is important because it can be harnessed to detect trace amounts of DNA as well as manipulate their motions in micro- and nano-scale biomedical devices¹. Recently, the dielectric spectra of short-chain DNA oligomers were measured, exhibiting an absorption peak corresponding to a 10ns timescale process². This is the first time such data is available for oligomers small enough to be accessible to detailed molecular dynamics simulations. The goal of our calculations is to confirm that theoretical models can reproduce this experimental feature, and to evaluate the conflicting interpretations of this feature which have been proposed in the literature. A molecular understanding of the link between DNA dynamics and dielectric response has eluded scientists for a long time because these properties are difficult to extract from experimental data. Probing these properties using simulations has proved difficult as well due to their large size and long time-scales associated with their motions. Hence one needs to accumulate very long trajectories, which requires large storage capabilities. We have re-formulated the theory in a way that enables calculation of dielectric properties from both equilibrium and non-equilibrium simulations using sparse sampling of data without compromising accuracy. The advantage of this is that we can use the same methodology to probe other biomolecules as well. We have shown proof-of-principle by calculating the electric field-induced flow of a simple electrolyte system, and the contribution of ions to its dielectric spectrum using our very sparse time sampling method. For DNA studies, we have accumulated an exceptionally long 5 microsecond trajectory for a DNA dodecamer in water. We have been successful in capturing the experimentally observed 10ns peak in the frequency dependent dielectric spectrum using our methods. We are currently in the process of characterising the different motions contributing to this spectrum. Preliminary data for this is presented.

References:

1. R. Holzel, Dielectric and dielectrophoretic properties of DNA. IET Nanobiotechnol., 2009, Vol. 3, Iss. 2, 28–45
2. Omori S. et al. Dielectric dispersion for short double-strand DNA. Physical Review E, 2006, 73, 050901(R)

In eukaryotic cells, DNA is packaged into chromatin and chromosomes where nucleosome is the basic packaging unit. Important life processes such as gene expression, DNA replication and repair requires DNA to be unwrapped from histone core so that functional proteins, such as transcription factors, RNA polymerases and repair enzymes can access their target sites which otherwise are sterically occluded. We developed a quantitative model to study this nucleosome unwrapping process. Through comparison to recent experiment on DNA origami hinge-nuclesome system (Jenny Le et al., 2016), we found that nucleosome is more likely to be unwrapped asymmetrically, which is different from the belief in existing nuclesome unwrapping experiments that usually assume symmetric unwrapping. We demonstrated that, compared to symmetric unwrapping, the asymmetric unwrapping will facilitate the unwrapping processes by lowering the free energy cost at a given unwrapping state (end-to-end distance of the nucleosome). We believe that our research has potential impact in the field of studies such as nucleosome dynamics, chromatin dynamics and regulatory processes involving nucleosome unwrapping.