Opposing roles of organic salts on mini-protein structure.

We investigated the effects of 1-ethyl-3-methylimidazolium chloride ([EMIM][Cl]) and choline chloride ([Chol][Cl]) on the local environment and conformational landscapes of Trp-cage and Trpzip4 mini-proteins using experimental and computational approaches. Fluorescence experiments and computational simulations revealed distinct behaviors of the mini-proteins in the presence of these organic salts. [EMIM][Cl] showed a strong interaction with Trp-cage, leading to fluorescence quenching and destabilization of its native structural interactions. Conversely, [Chol][Cl] had a negligible impact on Trp-cage fluorescence at low concentrations but increased it at high concentrations, indicating a stabilizing role. Computational simulations elucidated that [EMIM][Cl] disrupted the hydrophobic core packing and decreased proline-aromatic residue contacts in Trp-cage, resulting in a more exposed environment for Trp residues. In contrast, [Chol][Cl] subtly influenced the hydrophobic core packing, creating a hydrophobic environment near the tryptophan residues. Circular dichroism experiments revealed that [Chol][Cl] stabilized the secondary structure of both mini-proteins, although computational simulations did not show significant changes in secondary content at the explored concentrations. The simulations also demonstrated a more rugged free energy landscape for Trp-cage and Trpzip4 in [EMIM][Cl], suggesting destabilization of the tertiary structure for Trp-cage and secondary structure for Trpzip4. Similar fluorescence trends were observed for Trpzip4, with [EMIM][Cl] quenching fluorescence and exhibiting stronger interaction, while [Chol][Cl] increased the fluorescence at high concentrations. These findings highlight the interplay between [EMIM][Cl] and [Chol][Cl] with the mini-proteins and provide a detailed molecular-level understanding of how these organic salts impact the nearby surroundings and structural variations. Understanding such interactions is valuable for diverse applications, from biochemistry to materials science.

Recovery of enzyme structure and activity following rehydration from ionic liquid.

Long-term preservation of proteins at room temperature continues to be a major challenge. Towards using ionic liquids (ILs) to address this challenge, here we present a combination of experiments and simulations to investigate changes in lysozyme upon rehydration from IL mixtures using two imidazolium-based ILs (1-ethyl-3-methylimidazolium ethylsulfate, [EMIM][EtSO4] and 1-ethyl-3-methylimidazolium diethylphosphate, [EMIM][Et2PO4]). Various spectroscopic experiments and molecular dynamics simulations are performed to ascertain the structure and activity of lysozyme. Circular dichroism spectroscopy confirms that lysozyme maintains its secondary structure upon rehydration, even after 295 days. Increasing the IL concentration decreases the activity of lysozyme and is ultimately quenched at sufficiently high IL concentrations, but the rehydration of lysozyme from high IL concentrations completely restores its activity. Such rehydration occurs in the most common lysozyme activity assay, but without careful attention, this effect on the IL concentration can be overlooked. From simulations we observe occupation of [EMIM+] ions near the vicinity of the active site and the ligand-lysozyme complex is less stable in the presence of ILs, which results in the reduction of lysozyme activity. Upon rehydration, fast leaving of [EMIM+] is observed and the availability of active site is restored. In addition, suppression of structural fluctuations is also observed when in high IL concentrations, which also explains the decrease of activity. This structure suppression is recovered after undergoing rehydration. The return of native protein structure and activity indicates that after rehydration lysozyme returns to its original state. Our results also suggest a simple route to protein recovery following extended storage.

Dual mechanism of ionic liquid-induced protein unfolding.

Ionic liquids (ILs) are gaining attention as protein stabilizers and refolding additives. However, varying degrees of success with this approach motivates the need to better understand fundamental IL-protein interactions. A combination of experiment and simulation is used to investigate the thermal unfolding of lysozyme in the presence of two imidazolium-based ILs (1-ethyl-3-methylimidazolium ethylsulfate, [EMIM][EtSO4] and 1-ethyl-3-methylimidazolium diethylphosphate, [EMIM][Et2PO4]). Both ILs reduce lysozyme melting temperature Tm, but more gradually than strong denaturants. [EMIM][Et2PO4] lowers lysozyme Tm more readily than [EMIM][EtSO4], as well as requiring less energy to unfold the protein, as determined by the calorimetric enthalpy ΔH. Intrinsic fluorescence measurements indicate that both ILs bind to tryptophan residues in a dynamic mode, and furthermore, molecular dynamics simulations show a high density of [EMIM]+ near lysozyme's Trp62 residue. For both ILs approximately half of the [EMIM]+ cations near Trp62 show perfect alignment of their respective rings. The [EMIM]+ cations, having a "local" effect in binding to tryptophan, likely perturb a critically important Arg-Trp-Arg bridge through favorable π-π and cation-π interactions. Simulations show that the anions, [EtSO4]- and [Et2PO4]-, interact in a "global" manner with lysozyme, due to this protein's strong net positive charge. The anions also determine the local distribution of ions surrounding the protein. [Et2PO4]- is found to have a closer first coordination shell around the protein and stronger Coulomb interactions with lysozyme than [EtSO4]-, which could explain why the former anion is more destabilizing. Patching of ILs to the protein surface is also observed, suggesting there is no universal IL solvent for proteins, and highlighting the complexity of the IL-protein environment.

Living Supramolecular Polymerization of DNA.

Recently there have been notable synthetic successes in supramolecular polymerization. By contrast, it has long been known that DNA can undergo supramolecular polymerization (concatemerization). Concatemerization is a step-like polymerization and consequently suffers from broad molecular weight distributions and generally undesirable cyclization reactions. Here we demonstrate that another supramolecular polymerization of DNA, hybridization chain reaction (HCR), is in fact a living polymerization. After consumption of initial monomer, the polymerization can be continued with further addition of monomer, and the molecular weight can be varied by the ratio of monomer to initiator. In contrast to concatemerization, HCR produces polymers with narrow dispersity while avoiding cyclization. Identification of the living character of this supramolecular polymerization presents new opportunities in structural DNA nanotechnology and molecular biology.

Lysozyme Solubility and Conformation in Neat Ionic Liquids and Their Mixtures with Water.

The room temperature solubility of a number of model proteins is assessed for a diverse set of neat ionic liquids (ILs). For two soluble protein-IL pairs, lysozyme in [C2MIM][EtSO4] (1-ethyl-3-methylimidazolium ethylsulfate) and in [C2,4,4,4P][Et2PO4] (tributyl(ethyl)phosphonium diethylphosphate), protein solubility and structure at various temperatures are probed by dynamic light scattering (assessing dissolved molecular size), turbidimetry (reflecting degree of solubility), and Fourier transform infrared spectroscopy (uncovering helical secondary structure). As compared to aqueous environments, [C2,4,4,4P][Et2PO4] thermally stabilizes protein size and secondary structure while [C2MIM][EtSO4] does the opposite. Lysozyme denatured in [C2MIM][EtSO4] does not aggregate, presumably due to an absence of hydrophobic interactions, and the denaturation appears thermally reversible. Both ILs at room temperature are miscible with water in all proportions, but to create the corresponding ternary mixtures with protein, the order of mixing is important. Mixed to avoid additions of water to IL-dissolved protein, stable solutions are obtained with [C2MIM][EtSO4] at all solvent compositions. When water is added to IL-rich solutions, liquid-liquid demixing is noted.

Phage-based molecular probes that discriminate force-induced structural states of fibronectin in vivo.

Applied forces and the biophysical nature of the cellular microenvironment play a central role in determining cellular behavior. Specifically, forces due to cell contraction are transmitted into structural ECM proteins and these forces are presumed to activate integrin "switches." The mechanism of such switches is thought to be the partial unfolding of integrin-binding domains within fibronectin (Fn). However, integrin switches remain largely hypothetical due to a dearth of evidence for their existence, and relevance, in vivo. By using phage display in combination with the controlled deposition and extension of Fn fibers, we report the discovery of peptide-based molecular probes capable of selectively discriminating Fn fibers under different strain states. Importantly, we show that the probes are functional in both in vitro and ex vivo tissue contexts. The development of such tools represents a critical step in establishing the relevance of theoretical mechanotransduction events within the cellular microenvironment.

Aptamer-targeted DNA nanostructures for therapeutic delivery.

DNA-based nanostructures have been widely used in various applications due to their structural diversity, programmability, and uniform structures. Their intrinsic biocompatibility and biodegradability further motivates the investigation of DNA-based nanostructures as delivery vehicles. Incorporating AS1411 aptamers into DNA pyramids leads to enhanced intracellular uptake and selectively inhibits the growth of cancer cells, achieved without the use of transfection reagents. Furthermore, aptamer-displaying pyramids are found to be substantially more resistant to nuclease degradation than single-stranded aptamers. These findings, along with their modularity, reinforce the potential of DNA-based nanostructures for therapeutic applications.

Effects of short elastin-like peptides on filamentous particles and their transition behavior.

While elastin-like polypeptides and peptides (ELPs) have been used for various stimulus-responsive applications, details of their switching remain unclear. We therefore constructed a novel series of filamentous phage particles displaying a high surface density of short ELPs. The surface display of ELPs did not disrupt either particle shape or dimensions, and the resulting ELP-phage particles were colloidally stable over several weeks. However, in spite of a saturating surface density, macroscopic aggregation of ELP-phages cannot be triggered in water. To investigate the underlying mechanisms we examined conformational changes in the secondary structure of the phage proteins by circular dichroism and tryptophan fluorescence, which indicate partial protein unfolding in ELP-phage particles. To gain further insight into the ELP itself, analogous "free" ELP peptides were synthesized and characterized. Circular dichroism of these peptides shows the onset of ß-type conformations with increasing temperature, consistent with the accepted view of the microscopic transition that underlies the inverse phase behavior of ELPs. Increased guest residue hydrophobicity was found to depress the microscopic transition temperature of the peptides, also consistent with a previously proposed intramolecular hydrogen-bonding mechanism. Importantly, our results indicate that although the nanoscale presentation state can suppress macroscopic aggregation of ELPs, microscopic transitions of the ELP can still occur. Given the growing use of ELPs within supra-molecular scaffolds, such effects are important design considerations for future applications.

Charge screening between anionic and cationic surfactants in ionic liquids.

The aggregation and interfacial behavior of mixtures of anionic (sodium dodecylsulfate, SDS) and cationic (dodecylammonium bromide, DTAB) surfactants were investigated. A room-temperature ionic liquid (IL) was explored as a solvent for the SDS/DTAB system and compared to water. The critical micelle concentration (cmc) and composition in mixed micelles were determined for both solvents. Our experiments showed nearly ideal mixing of SDS/DTAB over the entire composition range and suggest that charge screening is prominent in ILs. This behavior is in sharp contrast to the strong electrostatic attraction and a multiphase composition gap in water. Two models by Clint and Rubingh, which describe ideal and nonideal micellar behavior, respectively, are discussed on the basis of our results. According to Rubingh's model, the composition of mixed micelles is gradually changing with the bulk composition in ILs but tends to be a 1:1 ratio in water. The results here are further support of the strong charge screening in ionic liquids.

Critical solution behavior of poly(N-isopropyl acrylamide) in ionic liquid-water mixtures.

The wide diversity of room-temperature ionic liquids (ILs) presents opportunities for studying, and controlling, polymer phase behavior. We have examined the phase behavior of poly(N-isopropyl acrylamide) (PNIPAM) in imidazolium ILs and their mixtures with water. We find there is a strong influence of the IL anion; specifically, the tetrafluoroborate anion yields a complex phase diagram with both LCST and UCST-type regimes. PNIPAM is generally miscible at intermediate IL-water compositions, although this range depends on the polymer molecular weight. Solvatochromatic characterization of both neat and mixed solvents reveals a key role for the interplay between PNIPAM-IL hydrogen-bonding and ion-pairing within the IL. These results demonstrate that appropriate selection of ILs should allow for increased control over polymer phase behavior.

The role of defects on the assembly and stability of DNA nanostructures.

Defects are known to underlie the mechanical properties of materials, especially so at the nanoscale. Using four compositionally identical DNA triangles, defect density is found to be inversely correlated with assembly efficiency and melting temperature. These findings are supported by a series of experiments with more complex DNA pyramids. Because they are naturally responsive to stresses, defects present an attractive opportunity as design elements for responsive DNA materials.

Solubility and aggregation of charged surfactants in ionic liquids.

Room-temperature ionic liquids (ILs) exhibit a unique set of properties, leading to opportunities for numerous applications. To obtain a better understanding of IL interfaces at a molecular level, we combined charged surfactants with ILs and studied their interfacial behavior. The critical micelle concentration (cmc) of each surfactant-IL pair was determined from both solubility phase diagrams and isotherms. Because the cmc is equivalent to the solubility at the Krafft temperature, a connection between the solubility of the surfactant and the physical properties of the underlying ionic liquid was established. Interfacial energy was found to be the major factor affecting the surfactant aggregation process, although its magnitude depends strongly on the IL structure. The results here give insight into explaining the nature of self-assembly of surfactants at IL interfaces and the interaction between solutes and IL solvents.

Design, assembly, and activity of antisense DNA nanostructures.

Discrete DNA nanostructures allow simultaneous features not possible with traditional DNA forms: encapsulation of cargo, display of multiple ligands, and resistance to enzymatic digestion. These properties suggested using DNA nanostructures as a delivery platform. Here, DNA pyramids displaying antisense motifs are shown to be able to specifically degrade mRNA and inhibit protein expression in vitro, and they show improved cell uptake and gene silencing when compared to linear DNA. Furthermore, the activity of these pyramids can be regulated by the introduction of an appropriate complementary strand. These results highlight the versatility of DNA nanostructures as functional devices.

Controlled interfacial assembly and transfer of brushlike copolymer films.

The self-assembly and compression of polybutadiene-bpoly(ethylene oxide) (PBd-PEO) at the air/water interface enables control over surface density, height, and film structure. Interfacial transfer was performed by a combination of Langmuir-Blodgett (LB) and Langmuir-Schaefer (LS) techniques, resulting in monolayer and bilayer films. Ellipsometry and wettability results were used to characterize the efficiency of transfer and to determine the properties of the resulting films, confirming a brushlike monolayer. Importantly, a high surface density is essential to obtain the desired film structure (i.e. a dense brush) and surface properties. The films were challenged by adsorption of fibrinogen, and the results are consistent with the notion of a PEO-enriched, and protein-repellant, bilayer surface. Such a bilayer film provides an opportunity for a tunable biomaterial interface to probe cell-surface interactions.

Biofunctional polymer nanoparticles for intra-articular targeting and retention in cartilage.

The extracellular matrix of dense, avascular tissues presents a barrier to entry for polymer-based therapeutics, such as drugs encapsulated within polymeric particles. Here, we present an approach by which polymer nanoparticles, sufficiently small to enter the matrix of the targeted tissue, here articular cartilage, are further modified with a biomolecular ligand for matrix binding. This combination of ultrasmall size and biomolecular binding converts the matrix from a barrier into a reservoir, resisting rapid release of the nanoparticles and clearance from the tissue site. Phage display of a peptide library was used to discover appropriate targeting ligands by biopanning on denuded cartilage. The ligand WYRGRL was selected in 94 of 96 clones sequenced after five rounds of biopanning and was demonstrated to bind to collagen II alpha1. Peptide-functionalized nanoparticles targeted articular cartilage up to 72-fold more than nanoparticles displaying a scrambled peptide sequence following intra-articular injection in the mouse.

Nuclear pores and membrane holes: generic models for confined chains and entropic barriers in pore stabilization.

The lumen of the nuclear pore complex is increasingly understood to be lined by a polymer brush that entropically regulates transport in and out of the nucleus-and it seems likely that similar effects probably arise with glycocalyx-lined holes in cell membranes. Here we mimic such pore-confined brushes with self-assembled polymer membranes imbued with nano-holes. Experiment and theory help elucidate the entropic origin and stabilization of the pores, which appear to have a similar basis as steric stabilization of colloids bearing polymer brushes. Free energies of interacting brushes reveal stable minima at pore sizes smaller than the classical metastable point, with little effect of the particular pore geometry. Such entropic forces have potential implications for lock and key mechanisms of nuclear pore assembly as well as transient poration of cells and synthetic nano-pores with regulatory mechanisms for transport.

Micelle co-assembly in surfactant/ionic liquid mixtures.

HYPOTHESIS: The phase behavior of amphiphiles is known to depend on their solvent environment. The organic character of ionic liquids suggested the possibility to tune surfactant aggregation, even in the absence of water, by selection of appropriate ionic liquid chemistry. To that end the behavior of the surfactant sodium dodecylsulfate in a chemically similar imidazolium ionic liquid, 1-ethyl-3-methyl imidazolium ethylsulfate, was explored. EXPERIMENTS: The solubility of sodium dodecylsulfate in 1-ethyl-3-methyl imidazolium ethylsulfate was determined, establishing the Krafft temperature. Tensiometry was performed to obtain interfacial properties such as the surface excess and area per molecule. Pulsed-field gradient spin-echo NMR was used to determine the diffusion coefficients of all the major species, including micelles, as a function of surfactant concentration. Importantly, all three methods provided consistent values for the critical micelle concentration. FINDINGS: Analysis of tensiometry data suggests, and is confirmed by NMR results, that the ionic liquid ions are incorporated along with surfactants into micelles, revealing a complex micellization behavior. In light of these findings past studies with ternary mixtures of surfactants, ionic liquids, and water may merit additional scrutiny. Given the large number of ionic liquids, this work suggests opportunities to further control micelle formation and properties.

DNA nanostructures: a shift from assembly to applications.

The specificity of DNA hybridization allows for the modular design of 2D and 3D shapes with wide-ranging applications including sensors, actuators, and even logic devices. The inherent biocompatibility of DNA and the ability to produce monodisperse structures of controlled shape and size make DNA nanostructures of interest as potential drug and gene delivery vehicles. In this review, we discuss several new approaches for the assembly of DNA nanostructures, advances in the modeling of these structures, and we highlight recent studies on the use of DNA nanotechnology for therapeutic applications such as drug delivery in tumor models.

Interplay of Dynamical Properties between Ionic Liquids and Ionic Surfactants: Mechanism and Aggregation.

The dynamical and aggregation behaviors of sodium dodecyl sulfate (SDS) in 1-ethyl-3-methylimidazolium ethylsulfate [EMIM+][EtSO4­] are characterized experimentally and computationally. A retardation of the ionic liquid (IL) and SDS diffusion coefficients with a concentration increase of SDS is observed. In agreement with experiments, aggregation is detected for concentrations higher than the experimental critical micelle concentration (CMC), which is mostly driven by alkyl tail aggregation. Solvent-exposed hydrophobic patches are observed on the micelle's surfaces. The hydrophobic tails of the IL molecules are found to fill those micelle's hydrophobic patches. Also, penetration of the IL is found in the SDS micelles, indicating that the IL acts as a cosurfactant, allowing the formation of "mixed" micelles. A higher level of Na+ counterion dissociation compared to previous studies of SDS micelles in aqueous solutions is also observed. A multilayering effect of alternating IL anions and cations is detected at the surface of the formed aggregates. The observed increase in system ordering with SDS concentration is what hinders the mobility of each chemical species.

Effects of prolonged ethanol lock exposure to carbothane- and silicone-based hemodialysis catheters: a 26-week study.

PURPOSE: Antibiotic locks in catheter-dependent chronic hemodialysis patients reduce the rate of catheter-related bloodstream infections (CRBSIs), but may be associated with the development of resistant bacteria. Ethanol-based catheter locks may provide a better alternative; however, there are limited data on the long-term integrity of dialysis catheters exposed to ethanol. METHODS: We performed in vitro testing of two types of hemodialysis catheters­silicone (SLC) and carbothane (CBT) based­with a 70% ethanol lock (EL) versus heparin lock (HL) for 26 weeks. Lock solutions were changed thrice weekly to mimic a conventional hemodialysis schedule. We tested mechanical properties of the catheters at 0, 13 and 26 weeks by examining stress/strain relationships (SS400%) and modulus of elasticity (ME). Electron microscopy was performed to examine catheter ultrastructure at 0 and 26 weeks. RESULTS: Catheter integrity for HL versus EL in SLC (SS400%: 4.5 vs. 4.5 MPa, p = NS; ME: 4.6 vs. 4.7 MPa, p = NS) or CBT-based catheters (SS400%: 7.6 vs. 8.9 MPa, p = NS; ME: 9.6 vs. 12.2 MPa, p = NS) were all similar at 13 and 26 weeks. Scanning electron microscopy revealed no structural changes in the central and luminal wall internal surfaces of EL- versus HL-treated catheters. CONCLUSIONS: There were no significant differences in catheter integrity between SLC or CBT catheters exposed to a 70% EL for 26 weeks. Given its low cost, potential to avoid antibiotic resistance and structural integrity after 6 months of high-dose ethanol, ELs should be studied prospectively against antibiotic locks to assess the efficacy and safety in hemodialysis patients.