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. We provided a detailed conformational analysis of model systems of CTD with different lengths; first with the last 44 residues of the human CTD sequence and finally the CTD model with 2-heptapeptide repeating units. We then investigated the effects of phosphorylation on CTD conformations by performing simulations at different phosphorylated states. We obtained broad conformational spaces in nonphosphorylated CTD models, and phosphorylation has complex effects on the conformations of the CTD. These complex effects depend on the length of the CTD, spacing between the multiple phosphorylation sites, ion coordination, and interactions with the nearby residues.

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 q-dependent structural relaxation time scales that are the same across the family. Our results show that this is not the case, and in fact, the relaxation of in-network charge alternation appears to be significantly affected by the presence of separate polar and apolar domains. However, we also find that if one was to assign weight factors to the relaxation of the structural motifs, charge alternation always contributes about the same amount (between 62.1 and 66.3%) across systems to the running integral of the stress tensor correlation function from which the shear viscosity is derived. Adjacency correlations between positive and negative moieties also contribute an identical amount if a prepeak is not present (about 38%) and a slightly smaller amount (about 28%) when intermediate range order exists. The prepeak only contributes about 6% to viscoelastic relaxation, highlighting that the dynamics of the smaller scale motifs is the most important.

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. This Letter attempts to provide a clear and visual connection between friction-associated with the dynamics of the structural motifs (in particular, the charge network)-and recent theoretical work by Yamaguchi linking the time-dependent viscosity of ILs to the decay of the charge alternation peak in the dynamic structure function. We propose that charge blurring associated with the loss of memory of where positive and negative charges are within networks is the key mechanism associated with viscosity in ILs. An IL will have low viscosity if a characteristic charge-blurring decorrelation time is low. With this in mind, engineering new low-viscosity ILs is reduced to understanding how to minimize this quantity.

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-OSO3- in the bulk and at the vacuum interface. We find that the vacuum interface affects only the nanometer length scale. This is in contrast to what we have recently found in ( J. Phys. Chem. Lett. , 2016 , 7 ( 19 ), 3785 - -3790 ) for isoelectronic C[8]-mim+/C[8]-OSO3-, where the interface effect is long ranged. Interestingly, ions with the diether tail functionality still favor the tail-outward orientation at the vacuum interface and the bulk phase preserves the alternation between charged networks and tails that is commonly observed for biphilic ionic liquids. However, such alternation is less well-defined and results in a significantly diminished first sharp diffraction peak in the bulk liquid structure function.