Characterization of the effects of phosphorylation by CK2 on the structure and binding properties of human HP1β

Proteins of the Heterochromatin Protein 1 (HP1) family are regulators of chromatin structure and genome function in eukaryotes. Post-translational modifications expand the repertoire of the chemical diversity of HP1 proteins and regulate their activity. Here, we investigated the effect of phosphorylation by Casein kinase 2 (CK2) on the structure, dynamics and binding activity of human HP1β. We show that Ser89 in the hinge region is the most effective substrate, followed by Ser175 at the C-terminal tail. Phosphorylation at these sites results in localized conformational changes in HP1β that do not compromise the ability of the protein to bind chromatin

Modeling the Structure of RNA Molecules with Small-Angle X-Ray Scattering Data

<div><p>We propose a novel fragment assembly method for low-resolution modeling of RNA and show how it may be used along with small-angle X-ray solution scattering (SAXS) data to model low-resolution structures of particles having as many as 12 independent secondary structure elements. We assessed this model-building procedure by using both artificial data on a previously proposed benchmark and publicly available data. With the artificial data, SAXS-guided models show better similarity to native structures than ROSETTA decoys. The publicly available data showed that SAXS-guided models can be used to reinterpret RNA structures previously deposited in the Protein Data Bank. Our approach allows for fast and efficient building of <i>de novo</i> models of RNA using approximate secondary structures that can be readily obtained from existing bioinformatic approaches. We also offer a rigorous assessment of the resolving power of SAXS in the case of small RNA structures, along with a small multimetric benchmark of the proposed method.</p></div

Model of 1U8D against native structure and SAXS envelope.

<p>Comparison of the red model, and green native structure for the longest modeled RNA, 1U8D. Even though shape (grey) would seem a weak restraint, topology and contacts within the model structure correspond closely to the native (similarity between the model to either native, or reconstructed shape).</p

Proposed models of stem loop 3 (HP3).

<p>Models (right) depending of input secondary structure (red from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078007#pone.0078007-Wassarman1" target="_blank">[12]</a> corresponding to secondary structure on the left, and green corresponding to secondary structure plot in the center from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078007#pone.0078007-Marz1" target="_blank">[13]</a>). Nucleotides in red are changes made for facilitating the production of HP3.</p

Benchmark results.

<p>Benchmark results.</p

SAXS model of stem loop 4 versus the NMR structure.

<p>The gray envelope is a shape reconstruction using SAXS data, the red is a model using SAXS data, and the green is an NMR-based structure deposited in PDB. Tails of the model and the native structure that do not share the common secondary structure, are marked with shades of grey.</p

SAXS data and fit for the model of HP4.

<p>Plots of SAXS data and fit to the model (dashed red line) of stem loop 4 (HP4) against gathered experimental data (blue line with gray error bars), and fit to the NMR model (green line). The data is shown with log-log data plot (A), Kratky plot showing that RNA is compact and folded (B), P(r) plot showing approximated distribution of interatomic distances within particle (C), and Guinier plot with shown , and fit.</p

Data parameters.

<p>Data parameters.</p

Tertiary structure elements broken down by topology.

<p>Nodes of this graph correspond directly to the nodes within the secondary structure graph presented in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078007#pone-0078007-g001" target="_blank">Figure 1</a>, so that three-dimensional element covers a single secondary structure element.</p