Decoupling of Interactions between Model-Charged Peptides Reveals Key Factors Responsible for Liquid-Liquid Phase Separation.

Liquid-liquid phase separation (LLPS) by disordered proteins has been shown to govern biological processes and cause numerous diseases. Therefore, a deeper understanding of the interactions and their variation with external factors is key to modulating the LLPS behavior of different systems and protecting proteins from pathological aggregation. In this context, we have looked at interactions between similarly charged peptides to understand the molecular features that may drive or prevent condensate formation under various conditions. We have studied dimer formation for model peptides where charged and noncharged amino acids have been placed alternatively. Using arginine and glutamic acid as the charged residues and varying the other residues with glycine, alanine, and proline to alter hydrophobicity, we have obtained the free-energy surface (FES) for the dimer formation for these systems under high salt concentration at two different temperatures using all-atom molecular dynamics simulations and the well-tempered metadynamics method. Our results indicate that a combination of effects such as hydrophobicity, arginine-arginine interactions, or water release from the solvation shell makes dimerization free energy more favorable for the positively charged peptides with lower flexibility. For the negatively charged peptides, the crucial role of water has been found in governing the FES. Systems having charged residues and phenylalanine in the peptide sequence also have been studied at high salt concentrations using unbiased simulations. In this case, only the positively charged peptides were found to aggregate through temperature-dependent hydrophobic and cation-π interactions. Overall, our study indicates that the negatively charged peptides are more likely to remain in the dilute phase under various conditions compared to the positively charged systems. The findings from our study would be helpful in designing and controlling systems to obtain LLPS behavior for therapeutic usage.

Identifying the Template for Oligomer to Fibril Conversion for Amyloid-ß (1-42) Oligomers using Hamiltonian Replica Exchange Molecular Dynamics.

The toxicity of amyloid-ß (Aß) oligomers has been known to be higher compared to mature fibrils. Yet the presence of plaques in Alzheimer's disease patients indicates the significance of oligomer to fibril conversion for Aß aggregates. In this study, we investigate Aß13-42 oligomers having two to five peptide chains using extensive all-atom molecular dynamics simulations to identify the on- or off-pathway intermediates in fibril formation pathway. Hamiltonian replica exchange method through solute tempering (REST2) has been employed to explore the different structures attained by these aggregates. Using intra-chain and inter-chain contacts as reaction coordinates, we obtain the free energy surface for the Aß13-42 oligomers. Consequently, their stable conformations and structural features have been identified. The found conformations belonging to most probable structures possess both parallel and anti-parallel ß-sheets, characteristic of on- and off-pathway intermediates, respectively. Further, we have measured the tendency to form fibril like interactions among the ß-sheet forming residues. Our analysis finds that residues 30-36 possess higher tendency to form fibril like contacts among all the residues. While we find stronger interaction among residues 30-36, these amino acids are also found to be more shielded from water compared to others. With previous experimental studies finding these residues to be more crucial for the stability of Aß42 oligomers, we propose that interactions within this patch could trigger seed formation that leads to conversion of on-pathway oligomers into disease relevant fibrils.

Kinetic and thermodynamic stability comparison for the fibrillar form of small amyloid-ß(1-42) oligomers using scaled molecular dynamics.

Amyloid-ß (Aß) oligomers act as intermediates for several neurodegenerative disease-relevant fibril formations. However, gaining insight into the oligomer to fibril conversion process remains a challenge due to the transient nature of small Aß. In this study, we probe the kinetic and thermodynamic stabilities of small Aß(1-42) oligomers in fibrillar conformations to understand from what size these aggregates start forming stable fibrils. With no definite structures available for small Aß42 aggregates, we have started with oligomers extracted from mature fibrils having four, five, six and nine chains stacked together, and have performed order-to-disorder transition on these systems. Using scaled molecular dynamics (sMD) simulation, the timescale for breaking the native contacts of fibrils has been compared. The results indicate that the kinetic stability of oligomers increases with size, especially at the C-terminus end beyond five-chain oligomers. The free energy of breaking the contacts at the ß-sheet regions in the structures has been obtained on an unscaled potential from a free energy extrapolation (FEE) approach. The values show that although stable minima are obtained for larger oligomers due to the enhanced stability of the C-terminus ends, fully stable fibril formation may require aggregates larger than the ones considered in our study. Additionally, dissimilar kinetics for the unbinding of terminal chains across all the oligomers has been observed. The interaction energy values calculated from unscaled MD simulations reveal the crucial role of water in our observations. Our work provides the application of an easy-to-deploy method that sheds light on interactions which could be significant in the early stages of Aß42 fibril formation.

Effect of water and ionic liquids on biomolecules.

The remarkable progress in the field of ionic liquids (ILs) in the last two decades has involved investigations on different aspects of ILs in various conditions. The nontoxic and biocompatible nature of ILs makes them a suitable substance for the storage and application of biomolecules. In this regard, the aqueous IL solutions have attracted a large number of studies to comprehend the role of water in modulating various properties of biomolecules. Here, we review some of the recent studies on aqueous ILs that concern the role of water in altering the behavior of ILs in general and in case of biomolecules solvated in ILs. The different structural and dynamic effects caused by water have been highlighted. We discuss the different modes of IL interaction that are responsible for stabilization and destabilization of proteins and enzymes followed by examples of water effect on this. The role of water in the case of nucleic acid storage in ILs, an area which has mostly been underrated, also has been emphasized. Our discussions highlight the fact that the effects of water on IL behavior are not general and are highly dependent on the nature of the IL under consideration. Overall, we aim to draw attention to the significance of water dynamics in the aqueous IL solutions, a better understanding of which can help in developing superior storage materials for application purposes.

pH-Gated Chloride Transport by a Triazine-Based Tripodal Semicage.

Triazine-based preorganized tripodal receptors are reported as efficient transmembrane Cl- carriers. These receptors were designed based on triazine core and 3,7-diazabicyclo[3.3.1]nonane arms to facilitate preorganized cavity formation. Each bicyclic arm was further functionalized to control protonation and lipophilicity, which are crucial for their efficient anion binding and effective transport through liposomal membranes. The benzyl-substituted receptor was the most effective ion transporter followed by the pentafluorobenzyl-substituted derivative. The nonsubstituted receptor was least active owing to its high polarity. Two active transporters were found to function as mobile carriers for Cl- via an antiport exchange mechanism. Molecular dynamic simulations with the most active receptor show a strong Cl- binding within the cavity by direct and water-mediated H-bonds with its N-H groups.

Water modulates the ultraslow dynamics of hydrated ionic liquids near CG rich DNA: consequences for DNA stability.

Ionic liquids are known to stabilize DNA for much longer than water can. While the source of this stability has commonly been attributed to thermodynamic aspects, we probe the dynamical aspects of the ionic liquids near DNA to further our understanding of this stability. Using molecular dynamics simulation, we calculated the mean residence time (MRT) of the cations of five different ionic liquids (ILs) in the grooves and around phosphate groups of AT and CG rich DNA segments. We find the residence time of different cations next to CG rich DNA to be much higher compared to that next to AT rich DNA, with a negligible difference with the variation of anions. The interaction energy between cations and DNA, however, shows exactly the opposite trend; it is much lower (indicating a stronger interaction) for AT than for CG. Investigation of DNA parameters reveals an insignificant difference for the DNA sequences under consideration. Analysis of water behavior provides a rationale for the long MRTs of cations; water molecules have been found to be denser and to possess higher MRT when next to CG-rich DNA, thus resulting in a crowded environment. Our results indicate that the dynamics influence the binding of ILs to different DNA sequences, possibly by modulating the entropy of the binding process.

One-Pot Synthesis and Transmembrane Chloride Transport Properties of C3-Symmetric Benzoxazine Urea.

One-pot synthesis of a C3-symmetric benzoxazine-based tris-urea compound is discussed. 1H NMR titrations indicate a stronger Cl- binding compared that of Br- and I- by the receptor. Effective Cl- transport across liposomal membranes via a Cl-/X- antiport mechanism is confirmed. Theoretical calculation suggests that a few water molecules with N-H, C═O, and the aromatic ring of the receptor create a H-bonded polar cavity where a Cl- is recognized by O-H···Cl- interactions from five bridged water molecules.

Impact of Ions on Individual Water Entropy.

Solutes determine the properties of a solution. In this study, we probe ionic solutions through the entropy of individual water molecules in the solvation shells around different cations and anions. Using a method recently developed by our group, we show the solvation shell entropy stemming from the individual contributions correlates extremely well with experimental values for both polarizable and nonpolarizable force fields. The behavior of water entropy as a function of distance reveals significant (∼20%) contributions from the second solvation shell even for the low concentration considered here. While for the cations, contributions from both translational and rotational entropy loss are similar in different solvation shells, water around anions loses much more rotational entropy due to their ability to accept hydrogen bonds. Most importantly, while charge density of cations or anions correlates with the translational entropy loss, anions with similar charge density as that of cations has a much stronger and long-range effect on water. We also show how the modulation of water entropy by ions is correlated to the structural modifications of hydration shell. This study thus provides a step toward understanding the entropic behavior of water in molecular recognition processes between proteins and drug molecules.

An Ultrahydrophobic Fluorous Metal-Organic Framework Derived Recyclable Composite as a Promising Platform to Tackle Marine Oil Spills.

Derived from a strategically chosen hexafluorinated dicarboxylate linker aimed at the designed synthesis of a superhydrophobic metal-organic framework (MOF), the fluorine-rich nanospace of a water-stable MOF (UHMOF-100) exhibits excellent water-repellent features. It registered the highest water contact angle (≈176°) in the MOF domain, marking the first example of an ultrahydrophobic MOF. Various experimental and theoretical studies reinforce its distinctive water-repellent characteristics, and the conjugation of superoleophilicity and unparalleled hydrophobicity of a MOF material has been coherently exploited to achieve real-time oil/water separation in recyclable membrane form, with significant absorption capacity performance. This is also the first report of an oil/water separating fluorinated ultrahydrophobic MOF-based membrane material, with potential promise for tackling marine oil spillages.

Chloride-Mediated Apoptosis-Inducing Activity of Bis(sulfonamide) Anionophores.

Transmembrane anion transport modality is enjoying a renewed interest because of recent advances toward anticancer therapy. Here we show bis(sulfonamides) as efficient receptors for selective Cl(-) ion binding and transport across lipid bilayer membranes. Anion-binding studies by (1)H NMR indicate a logical correlation between the acidity of sulfonamide N-H proton and binding strength. Such recognition is influenced further by the lipophilicity of a receptor during the ion-transport process. The anion-binding and transport activity of a bis(sulfonamide) system are far superior compared to those of the corresponding bis(carboxylic amide) derivative. Fluorescent-based assays confirm the Cl(-)/anion antiport as the operational mechanism of the ion transport by bis(sulfonamides). Disruption of ionic homeostasis by the transported Cl(-) ion, via bis(sulfonamide), is found to impose cell death. Induction of a caspase-dependent intrinsic pathway of apoptosis is confirmed by monitoring the changes in mitrochondrial membrane potential, cytochrome c leakage, activation of family of caspases, and nuclear fragmentation studies.

Distribution of Residence Time of Water around DNA Base Pairs: Governing Factors and the Origin of Heterogeneity.

Water dynamics in the solvation shell around biomolecules plays a vital role in their stability, function, and recognition processes. Although extensively studied through various experimental and computational methods, dynamical time scales of water near DNA is highly debated. The residence time of water is one such dynamical quantity that has been probed rarely around DNA using computational methods. Moreover, the effect of local DNA sequence variation in water residence time has also not been addressed. Using 20 DNA systems with different sequences, we capture here the mean residence time (MRT) of water molecules around 360 different sites in the major and minor grooves of DNA. Thus, we show that a distribution of time scales exists even for a regular structure of DNA, reflecting the effect of chemistry, topography, and other factors governing dynamics of water. We used the stable state picture (SSP) formalism to calculate MRT that avoids the effect of transient recrossing. Results obtained from simulations agree well with experiments done on a few specific systems at a similar temperature. Most importantly, we find that although the groove width and depth influence water time scale, MRT of water is always longer in the middle of the DNA, in agreement with NMR experiments. We propose a simple kinetic model of water escape from DNA where water molecules move along the DNA and perpendicular to it in both the first and second solvation shell before it escapes to bulk. We show that this simple kinetic model captures both the time scale and the position dependence of MRT of water around DNA. This study thus portrays the origin and a measure of heterogeneity in water dynamics around DNA and provides a fresh perspective in the ongoing debate on water dynamical time scales around DNA.