Effect of Pressure on the Conformational Landscape of Human γD-Crystallin from Replica Exchange Molecular Dynamics Simulations.

Human γD-crystallin belongs to a crucial family of proteins known as crystallins located in the fiber cells of the human lens. Since crystallins do not undergo any turnover after birth, they need to possess remarkable thermodynamic stability. However, their sporadic misfolding and aggregation, triggered by environmental perturbations or genetic mutations, constitute the molecular basis of cataracts, which is the primary cause of blindness in the globe according to the World Health Organization. Here, we investigate the impact of high pressure on the conformational landscape of wild-type HγD-crystallin using replica exchange molecular dynamics simulations augmented with principal component analysis. We find pressure to have a modest impact on global measures of protein stability, such as root-mean-square displacement and radius of gyration. Upon projecting our trajectories along the first two principal components from principal component analysis, however, we observe the emergence of distinct free energy basins at high pressures. By screening local order parameters previously shown or hypothesized as markers of HγD-crystallin stability, we establish correlations between a tyrosine-tyrosine aromatic contact within the N-terminal domain and the protein's end-to-end distance with projections along the first and second principal components, respectively. Furthermore, we observe the simultaneous contraction of the hydrophobic core and its intrusion by water molecules. This exploration sheds light on the intricate responses of HγD-crystallin to elevated pressures, offering insights into potential mechanisms underlying its stability and susceptibility to environmental perturbations, crucial for understanding cataract formation.

Reduced graphene oxide/ionic liquid composites with tunable interlayer spacing for improved charge/discharge kinetics in supercapacitors.

The large specific surface area and high conductivity of reduced graphene oxide (RGO) make it a promising material for supercapacitors. However, aggregation of graphene sheets into graphitic domains upon drying hampers supercapacitor performance by drastically impeding ion transport inside electrodes. Here, we present a facile approach to optimize charge storage performance in RGO-based supercapacitors by systematically tuning their micropore structure. To this end, we combine RGOs with room temperature ionic liquids during electrode processing to impede stacking of sheets into graphitic structures with small interlayer distance. In this process, RGO sheets function as the active electrode material while ionic liquid serves both as a charge carrier and a spacer to control interlayer spacing inside electrodes and form ion transport channels. We show that composite RGO/ionic liquid electrodes with larger interlayer spacing and more ordered structure exhibit improved capacitance and charging kinetics.

Formation of dissipative structures in microscopic models of mixtures with species interconversion.

The separation of substances into different phases is ubiquitous in nature and important scientifically and technologically. This phenomenon may become drastically different if the species involved, whether molecules or supramolecular assemblies, interconvert. In the presence of an external force large enough to overcome energetic differences between the interconvertible species (forced interconversion), the two alternative species will be present in equal amounts, and the striking phenomenon of steady-state, restricted phase separation into mesoscales is observed. Such microphase separation is one of the simplest examples of dissipative structures in condensed matter. In this work, we investigate the formation of such mesoscale steady-state structures through Monte Carlo and molecular dynamics simulations of three physically distinct microscopic models of binary mixtures that exhibit both equilibrium (natural) interconversion and a nonequilibrium source of forced interconversion. We show that this source can be introduced through an internal imbalance of intermolecular forces or an external flux of energy that promotes molecular interconversion, possible manifestations of which could include the internal nonequilibrium environment of living cells or a flux of photons. The main trends and observations from the simulations are well captured by a nonequilibrium thermodynamic theory of phase transitions affected by interconversion. We show how a nonequilibrium bicontinuous microemulsion or a spatially modulated state may be generated depending on the interplay between diffusion, natural interconversion, and forced interconversion.

Origin of Enhanced Performance in Nanoporous Electrical Double Layer Capacitors: Insights on Micropore Structure and Electrolyte Composition from Molecular Simulations.

We explore the effect of solvation and micropore structure on the energy storage performance of electrical double layer capacitors using constant potential molecular dynamics simulations of realistically modeled nanoporous carbon electrodes and ionic liquid/organic solvent mixtures. We show that the time-dependent charging profiles of electrodes with larger pores reach the plateau regime faster, while the charging time has a nonmonotonic dependence on ion concentration, mirroring the composition dependence of bulk electrolyte conductivity. When the average pore size of the electrode is similar to or slightly larger than the size of a solvated ion, the solvation enhances ion electrosorption into nanopores by disrupting anion-cation coordination and decreasing the barrier to counterion penetration while blocking the co-ions. In these systems, areal capacitance exhibits a significant nonmonotonic dependence on ion concentration, in which capacitance increases with the introduction of solvent in the concentrated regime followed by a decrease with further dilution. This gives rise to a maximum in capacitance at intermediate dilution levels. When pores are significantly larger than solvated ions, capacitance maximum weakens and eventually disappears. These findings provide novel insights on the combined effect of electrolyte composition and electrode pore size on the charging kinetics and equilibrium behavior of realistically modeled electrical double layer capacitors. Generalization of the approach developed here can facilitate the rational optimization of material properties for electrical double layer capacitor applications.

Interconversion-controlled liquid-liquid phase separation in a molecular chiral model.

Liquid-liquid phase separation of fluids exhibiting interconversion between alternative states has been proposed as an underlying mechanism for fluid polyamorphism and may be of relevance to the protein function and intracellular organization. However, molecular-level insight into the interplay between competing forces that can drive or restrict phase separation in interconverting fluids remains elusive. Here, we utilize an off-lattice model of enantiomers with tunable chiral interconversion and interaction properties to elucidate the physics underlying the stabilization and tunability of phase separation in fluids with interconverting states. We show that introducing an imbalance in the intermolecular forces between two enantiomers results in nonequilibrium, arrested phase separation into microdomains. We also find that in the equilibrium case, when all interaction forces are conservative, the growth of the phase domain is restricted only by the system size. In this case, we observe phase amplification, in which one of the two alternative phases grows at the expense of the other. These findings provide novel insights on how the interplay between dynamics and thermodynamics defines the equilibrium and steady-state morphologies of phase transitions in fluids with interconverting molecular or supramolecular states.

Stability of Protein Structure during Nanocarrier Encapsulation: Insights on Solvent Effects from Simulations and Spectroscopic Analysis.

The dosing of peptide and protein therapeutics is complicated by rapid clearance from the blood pool and poor cellular membrane permeability. Encapsulation into nanocarriers such as liposomes or polymersomes has long been explored to overcome these limitations, but manufacturing challenges have limited clinical translation by these approaches. Recently, inverse Flash NanoPrecipitation (iFNP) has been developed to produce highly loaded polymeric nanocarriers with the peptide or protein contained within a hydrophilic core, stabilized by a hydrophobic polymer shell. Encapsulation of proteins with higher-order structure requires understanding how processing may affect their conformational state. We demonstrate a combined experimental/simulation approach to characterize protein behavior during iFNP processing steps using the Trp-cage protein TC5b as a model. Explicit-solvent fully atomistic molecular dynamics simulations with enhanced sampling techniques are coupled with two-dimensional heteronuclear multiple-quantum coherence nuclear magnetic resonance spectroscopy (2D-HMQC NMR) and circular dichroism to determine the structure of TC5b during mixed-solvent exposure encountered in iFNP processing. The simulations involve atomistic models of mixed solvents and protein to capture the complexity of the hydrogen bonding and hydrophobic interactions between water, dimethylsulfoxide (DMSO), and the protein. The combined analyses reveal structural unfolding of the protein in 11 M DMSO but confirm complete refolding after release from the polymeric nanocarrier back into an aqueous phase. These results highlight the insights that simulations and NMR provide for the formulation of proteins in nanocarriers.

Computational Investigation of the Effect of Pressure on Protein Stability.

Previous studies show parabolic or elliptical regions of protein stability in the pressure-temperature ( P, T) plane. The construction of stability diagrams requires accessing a sufficiently broad ( P, T) range, which is often frustrated by ice formation in experiments and sampling challenges in simulations. We perform a fully atomistic computational study of the miniprotein Trp-cage over the range of temperatures 210 ≤ T ≤ 420 K and pressures P ≤ 5 kbar and construct the corresponding stability diagram. At ambient temperature, pressure shifts the conformational states toward unfolding. Below 250 K, the native fold's stability depends nonmonotonically on pressure. While cold unfolding and thermal denaturation differ significantly at ambient pressure, they exhibit progressive similarity at elevated pressures. At ambient pressure, cold denaturation is an enthalpically driven process that preserves significant elements of Trp-cage's secondary structure. In contrast, cold unfolding at elevated pressures involves a more substantial loss of secondary and tertiary structure, similar to thermal denaturation.

Pattern of property extrema in supercooled and stretched water models and a new correlation for predicting the stability limit of the liquid state.

Water exhibits anomalous behavior in its supercooled region. A widely invoked hypothesis to explain supercooled water's thermodynamic anomalies is the existence of a metastable liquid-liquid transition terminating at a critical point. In this work, we analyze previously published and new simulation results for three commonly used molecular water models (ST2, TIP4P/2005, and TIP5P) that support the existence of the metastable liquid-liquid transition. We demonstrate that a corresponding-states-like rescaling of pressure and temperature results in a significant degree of universality in the pattern of extrema loci of the density, isothermal compressibility, and isobaric heat capacity. We also report, for the first time, an intriguing correlation between the location of the liquid-liquid critical point, the rescaled locus of density extrema, and the stability limit of the liquid state with respect to the vapor. A similar correlation is observed for two theoretical models that also exhibit a second (liquid-liquid) critical point, namely, the van der Waals and lattice-gas "two-structure" models. This new correlation is used to explore the stability limit of the liquid state in simultaneously supercooled and stretched water.

A Computational Study of the Ionic Liquid-Induced Destabilization of the Miniprotein Trp-Cage.

Fundamental understanding of protein stability away from physiological conditions is important due to its evolutionary implications and relevance to industrial processing and storage of biological materials. The molecular mechanisms of stabilization/destabilization by environmental perturbations are incompletely understood. We use replica-exchange molecular dynamics simulations and thermodynamic analysis to investigate the effects of ionic liquid-induced perturbations on the folding/unfolding thermodynamics of the Trp-cage miniprotein. We find that ionic liquid-induced denaturation resembles cold unfolding, where the unfolded states are populated by compact, partially folded structures in which elements of the secondary structure are conserved, while the tertiary structure is disrupted. Our simulations show that the intrusion of ions and water into Trp-cage's hydrophobic core is facilitated by the disruption of its salt bridge and 310-helix by specific ion-residue interactions. Despite the swelling and widening of the hydrophobic core, however, Trp-cage's α-helix remains stable. We further show that ionic liquid disrupts protein-protein and protein-water hydrogen bonds while favoring the formation of ion-protein bonds, shifting the equilibrium of conformational states and promoting denaturation near room temperature.

Concentration Fluctuations and Capacitive Response in Dense Ionic Solutions.

We use molecular dynamics simulations in a constant potential ensemble to study the effects of solution composition on the electrochemical response of a double layer capacitor. We find that the capacitance first increases with ion concentration following its expected ideal solution behavior but decreases upon approaching a pure ionic liquid in agreement with recent experimental observations. The nonmonotonic behavior of the capacitance as a function of ion concentration results from the competition between the independent motion of solvated ions in the dilute regime and solvation fluctuations in the concentrated regime. Mirroring the capacitance, we find that the characteristic decay length of charge density correlations away from the electrode is also nonmonotonic. The correlation length first decreases with ion concentration as a result of better electrostatic screening but increases with ion concentration as a result of enhanced steric interactions. When charge fluctuations induced by correlated ion-solvent fluctuations are large relative to those induced by the pure ionic liquid, such capacitive behavior is expected to be generic.

Anomalous Capacitance Maximum of the Glassy Carbon-Ionic Liquid Interface through Dilution with Organic Solvents.

We use electrochemical impedance spectroscopy to measure the effect of diluting a hydrophobic room temperature ionic liquid with miscible organic solvents on the differential capacitance of the glassy carbon-electrolyte interface. We show that the minimum differential capacitance increases with dilution and reaches a maximum value at ionic liquid contents near 5-10 mol% (i.e., ∼1 M). We provide evidence that mixtures with 1,2-dichloroethane, a low-dielectric constant solvent, yield the largest gains in capacitance near the open circuit potential when compared against two traditional solvents, acetonitrile and propylene carbonate. To provide a fundamental basis for these observations, we use a coarse-grained model to relate structural variations at the double layer to the occurrence of the maximum. Our results reveal the potential for the enhancement of double-layer capacitance through dilution.