Clustering of RNA Polymerase II C-Terminal Domain Models upon Phosphorylation.

RNA polymerase II (Pol II) C-terminal domain (CTD) is known to have crucial roles in regulating transcription. CTD has also been highly recognized for undergoing phase separation, which is further associated with its regulatory functions. However, the molecular interactions that the CTD forms to induce clustering to drive phase separations and how the phosphorylation of the CTD affects clustering are not entirely known.

Complex Conformational Space of the RNA Polymerase II C-Terminal Domain upon Phosphorylation.

Intrinsically disordered proteins (IDPs) have been closely studied during the past decade due to their importance in many biological processes. The disordered nature of this group of proteins makes it difficult to observe its full span of the conformational space using either experimental or computational studies. In this article, we explored the conformational space of the C-terminal domain (CTD) of RNA polymerase II (Pol II), which is also an intrinsically disordered low complexity domain, using enhanced sampling methods.

Relationship between the Relaxation of Ionic Liquid Structural Motifs and That of the Shear Viscosity.

In a set of recent articles, we have highlighted that friction is highly inhomogeneous in a typical ionic liquid (IL) with charge networks that are stiff and charge-depleted regions that are soft. This has consequences not only for the dynamics of ILs but also for the transport properties of solutes dissolved in them. In this article, we explore whether the family of alkylimidazolium ILs coupled with bis(trifluoromethylsulfonyl)imide (with similar Coulombic interactions but different alkyl tails), when dynamically "equalized" by having a similar shear viscosity, display -dependent structural relaxation time scales that are the same across the family.

A Pictorial View of Viscosity in Ionic Liquids and the Link to Nanostructural Heterogeneity.

Prototypical ionic liquids (ILs) are characterized by three structural motifs associated with (1) vicinal interactions, (2) the formation of positive-negative charge-alternating chains or networks, and (3) the alternation of these networks with apolar domains. In recent articles, we highlighted that the friction and mobility in these systems are nowhere close to being spatially homogeneous. This results in what one could call mechanical heterogeneity, where charge networks are intrinsically stiff and charge-depleted regions are softer, flexible, and mobile.

Ionic Liquids with Symmetric Diether Tails: Bulk and Vacuum-Liquid Interfacial Structures.

The behavior in the bulk and at interfaces of biphilic ionic liquids in which either the cation or anion possesses moderately long alkyl tails is to a significant degree well understood. Less clear is what happens when both the cation and anion possess tails that are not apolar, such as in the case of ether functionalities. The current article discusses the structural characteristics of C2OC2OC2-mim/C2OC2OC2-OSO in the bulk and at the vacuum interface.

Structures of Ionic Liquids Having Both Anionic and Cationic Octyl Tails: Lamellar Vacuum Interface vs Sponge-Like Bulk Order.

Numerous experimental and computational studies have shown that the structure of ionic liquids is significantly influenced by confinement and by interactions with interfaces. The nature of the interface can affect the immediate ordering of cations and anions, changing important rheological characteristics relevant to lubrication. Most studies suggest that such changes are local or short-ranged and that bulk properties are reestablished on a length scale of a few nanometers.