Designing Electrostatic Interactions via Polyelectrolyte Monomer Sequence

Charged polymers are ubiquitous in biological systems because electrostatic interactions can drive complicated structure formation and respond to environmental parameters such as ionic strength and pH. In these systems, function emerges from sophisticated molecular design; for example, intrinsically disordered proteins leverage specific sequences of monomeric charges to control the formation and function of intracellular compartments known as membraneless organelles. The role of a charged monomer sequence in dictating the strength of electrostatic interactions remains poorly understood despite extensive evidence that sequence is a powerful tool biology uses to tune soft materials. In this article, we use a combination of theory, experiment, and simulation to establish the physical principles governing sequence-driven control of electrostatic interactions. We predict how arbitrary sequences of charge give rise to drastic changes in electrostatic interactions and correspondingly phase behavior. We generalize a transfer matrix formalism that describes a phase separation phenomenon known as “complex coacervation” and provide a theoretical framework to predict the phase behavior of charge sequences. This work thus provides insights into both how charge sequence is used in biology and how it could be used to engineer properties of synthetic polymer systems

Sequence and Entropy-Based Control of Complex Coacervates

Biomacromolecules rely on the precise placement of monomers to encode information for structure, function, and physiology. Efforts to emulate this complexity via the synthetic control of chemical sequence in polymers are finding success; however, there is little understanding of how to translate monomer sequence to physical material properties. Here we establish design rules for implementing this sequence-control in materials known as complex coacervates. These materials are formed by the associative phase separation of oppositely charged polyelectrolytes into polyelectrolyte dense (coacervate) and polyelectrolyte dilute (supernatant) phases. We demonstrate that patterns of charges can profoundly affect the charge–charge associations that drive this process. Furthermore, we establish the physical origin of this pattern-dependent interaction: there is a nuanced combination of structural changes in the dense coacervate phase and a 1D confinement of counterions due to patterns along polymers in the supernatant phase

The Effect of Comb Architecture on Complex Coacervation

Complex coacervation is a widely utilized technique for effecting phase separation, though predictive understanding of molecular-level details remains underdeveloped. Here, we couple coarse-grained Monte Carlo simulations with experimental efforts using a polypeptide-based model system to investigate how a comb-like architecture affects complex coacervation and coacervate stability. Specifically, the phase separation behavior of linear polycation-linear polyanion pairs was compared to that of comb polycation-linear polyanion and comb polycation-comb polyanion pairs. The comb architecture was found to mitigate cooperative interactions between oppositely charged polymers, as no discernible phase separation was observed for comb-comb pairs and complex coacervation of linear-linear pairs yielded stable coacervates at higher salt concentration than linear-comb pairs. This behavior was attributed to differences in counterion release by linear vs. comb polymers during polyeletrolyte complexation. Additionally, the comb polycation formed coacervates with both stereoregular poly(L-glutamate) and racemic poly(D,L-glutamate), whereas the linear polycation formed coacervates only with the racemic polyanion. In contrast, solid precipitates were obtained from mixtures of stereoregular poly(L-lysine) and poly(L-glutamate). Moreover, the formation of coacervates from cationic comb polymers incorporating up to ~90% pendant zwitterionic groups demonstrated the potential for inclusion of comonomers to modulate the hydrophilicity and/or other properties of a coacervate-forming polymer. These results provide the first detailed investigation into the role of polymer architecture on complex coacervation using a chemically and architecturally well-defined model system, and highlight the need for additional research on this topic

Regulation of MicroRNA Biogenesis: A miRiad of mechanisms

microRNAs are small, non-coding RNAs that influence diverse biological functions through the repression of target genes during normal development and pathological responses. Widespread use of microRNA arrays to profile microRNA expression has indicated that the levels of many microRNAs are altered during development and disease. These findings have prompted a great deal of investigation into the mechanism and function of microRNA-mediated repression. However, the mechanisms which govern the regulation of microRNA biogenesis and activity are just beginning to be uncovered. Following transcription, mature microRNA are generated through a series of coordinated processing events mediated by large protein complexes. It is increasingly clear that microRNA biogenesis does not proceed in a 'one-size-fits-all' manner. Rather, individual classes of microRNAs are differentially regulated through the association of regulatory factors with the core microRNA biogenesis machinery. Here, we review the regulation of microRNA biogenesis and activity, with particular focus on mechanisms of post-transcriptional control. Further understanding of the regulation of microRNA biogenesis and activity will undoubtedly provide important insights into normal development as well as pathological conditions such as cardiovascular disease and cancer

High charge density coacervate assembly via hybrid monte carlo single chain in mean field theory

by Tyler K. Lytle, Mithun Radhakrishna and Charles E. Sin

Structure of the B3 domain from Arabidopsis thaliana protein At1g16640

A novel DNA binding motif, the B3 domain, has been identified in a number of transcription factors specific to higher plant species, and was recently found to define a new protein fold. Here we report the second structure of a B3 domain, that of the Arabidopsis thaliana protein, At1g16640. As part of an effort to ‘rescue’ structural genomics targets deemed unsuitable for structure determination as full-length proteins, we applied a combined bioinformatic and experimental strategy to identify an optimal construct containing a predicted conserved domain. By screening a series of N- and C-terminally truncated At1g16640 fragments, we isolated a stable folded domain that met our criteria for structural analysis by NMR spectroscopy. The structure of the B3 domain of At1g16640 consists of a seven-stranded β-sheet arranged in an open barrel and two short α-helices, one at each end of the barrel. While At1g16640 is quite distinct from previously characterized B3 domain proteins in terms of amino acid sequence similarity, it adopts the same novel fold that was recently revealed by the RAV1 B3 domain structure. However, putative DNA-binding elements conserved in B3 domains from the RAV, ARF, and ABI3/VP1 subfamilies are largely absent in At1g16640, perhaps suggesting that B3 domains could function in contexts other than transcriptional regulation