Flipping out: role of arginine in hydrophobic interactions and biological formulation design

Arginine has been a mainstay in biological formulation development for decades. To date, the way arginine modulates protein stability has been widely studied and debated. Here, we employed a hydrophobic polymer to decouple hydrophobic effects from other interactions relevant to protein folding. While existing hypotheses for the effects of arginine can generally be categorized as either direct or indirect, our results indicate that direct and indirect mechanisms of arginine co-exist and oppose each other. At low concentrations, arginine was observed to stabilize hydrophobic polymer folding via a sidechain-dominated direct mechanism, while at high concentrations, arginine stabilized polymer folding via a backbone-dominated indirect mechanism. Upon introducing partially charged polymer sites, arginine destabilized polymer folding. Further, we found arginine-induced destabilization of a model virus similar to direct-mechanism destabilization of the charged polymer and concentration-dependent stabilization of a model protein similar to the indirect mechanism of hydrophobic polymer stabilization. These findings highlight the modular nature of the widely used additive arginine, with relevance in the information-driven design of stable biological formulations.

Unravelling the optical properties and self-assembly behavior of ciprofloxacin in ionic liquid environments: probing the role of cationic residues and counter anions

This study investigated the interaction of ciprofloxacin (CIP) with three different ionic liquids (ILs) featuring distinct cationic residues (pyrrolidinium, IL1, vs. imidazolium, IL2, with bis(trifluoromethylsulfonyl)imide as the counter anion) and counter anions bis(trifluoromethylsulfonyl)imide, IL2, vs. hexafluorophosphate, IL3, with imidazolium as the cationic residue) in an aqueous environment. A series of spectroscopic studies have been performed to elucidate the role of ILs in the optical properties as well as aggregation behavior of CIP. The fluorescence quenching experiment indicated that the IL with a pyrrolidinium residue showed stronger binding with CIP, while bis(trifluoromethylsulfonyl)imide was the preferred anion. These quenching effects might be attributed to complex formation mediated by charge-pair and cation-π interactions, along with hydrogen bonding. The Stern-Volmer analysis confirmed a static quenching mechanism, with binding constants (Kb) reflecting the stronger affinity of IL1 due to the hydrophobic butyl group and the flexible pyrrolidinium cation, resulting in the formation of larger aggregates. In contrast, the imidazolium residue in IL2 facilitated π-π and hydrogen-bond interactions, disrupting CIP aggregation and resulting in smaller clusters. The polarizable nature of bis(trifluoromethylsulfonyl)imide along with its hydrogen bond-accepting ability enabled stronger binding of ILs containing this anion to CIP compared to hexafluorophosphate-containing ILs. Further studies indicated that pH 6 is optimum for CIP-IL interactions, where CIP remained in its zwitterionic form. Increased temperature and ionic strength diminished the quenching efficiency, consistent with the reduced stability of CIP-IL complexes under such conditions.

Visualization of Self-Assembly and Hydration of a β-Hairpin through Integrated Small and Wide-Angle Neutron Scattering

Fundamental understanding of the structure and assembly of nanoscale building blocks is crucial for the development of novel biomaterials with defined architectures and function. However, accessing self-consistent structural information across multiple length scales is challenging. This limits opportunities to exploit atomic scale interactions to achieve emergent macroscale properties. In this work we present an integrative small- and wide-angle neutron scattering approach coupled with computational modeling to reveal the multiscale structure of hierarchically self-assembled β hairpins in aqueous solution across 4 orders of magnitude in length scale from 0.1 Å to 300 nm. Our results demonstrate the power of this self-consistent cross-length scale approach and allows us to model both the large-scale self-assembly and small-scale hairpin hydration of the model β hairpin CLN025. Using this combination of techniques, we map the hydrophobic/hydrophilic character of this model self-assembled biomolecular surface with atomic resolution. These results have important implications for the multiscale investigation of aqueous peptides and proteins, for the prediction of ligand binding and molecular associations for drug design, and for understanding the self-assembly of peptides and proteins for functional biomaterials.

Does Urea Preferentially Interact with Amide Moieties or Nonpolar Sidechains? A Question Answered Through a Judicious Selection of Model Systems

The transfer model suggests that urea unfolds proteins mainly by increasing the solubility of the amide backbone, probably through urea-induced increase in hydrogen bonding. Other studies suggest that urea addition increases the magnitude of solvent-solute van der Waals interactions, which increases the solubility of nonpolar sidechains. More recent analyses hypothesize that urea has a similar effect in increasing the solubility of backbone and sidechain groups. In this work, we compare the effects of urea addition on the solvation of amides and alkyl groups. At first, we study the effects of urea addition upon solvent hydrogen bonding acidity and basicity through the perturbation in the fluorescence spectrum of probes 1-AN and 1-DMAN. Our results demonstrate that the solvent's hydrogen bonding properties are minimally affected by urea addition. Subsequently, we show that urea addition does not perturb the intra-molecular hydrogen bonding in salicylic acid significantly. Finally, we investigate how urea preferentially interacts with amide and alkyl groups moieties in water by comparing the effects of urea addition upon the solubility of acetaminophen and 4-tertbutylphenol. We show that urea affects amide and t-butyl solubility (lowers the transfer free energy of both amide (backbone) and alkyl (sidechain) groups) in a similar fashion. In other words, preferential interaction of urea with both moieties contributes to protein denaturation.

Evaluation and characterization of starch nanoparticles for adsorption of urea from dialysates

Starch nanoparticles (SNPs) was produced from type-A, B and C native starches (corn, potato and Trichosanthes kirilowii pulp starches respectively), via the nanoprecipitation method. The SNPs showed different amylose contents, water contact angles, surface morphologies and urea clearance performances. In this work, to examine the parameters of SNPs that may change the urea adsorption capacity, urea adsorption performance in adsorption environments with different pH values, urea concentrations, and adsorption times was examined. Thereafter, the characteristics of SNPs were tested by water contact angle measurements (WCA), transmission electron microscopy, specific surface area measurements, gel permeation chromatography, and zeta potential analysis. The results showed that the Trichosanthes kirilowii pulp (C) SNPs show better adsorption than the corn (A) and potato (B) SNPs. The hydrophobicity of SNPs promotes the urea adsorption of the SNPs. Using grey relational analysis, it was found that WCA and Mn are the critical parameter affecting the adsorption performance, with WCA and Mn within the ranges of 31-33° and 1900-2100 kDa, respectively, were found to be the conditions for optimal urea adsorption.

Effect of urea on the hydration and aggregation of hydrophobic and amphiphilic solute models: Implications to protein aggregation

Despite the emergence of a molecular picture of urea's protein unfolding mechanism in the past few decades, less is known about its action mechanism on protein aggregation. This is especially relevant for understanding the aggregation of amyloid proteins and peptides, implicated in several neurodegenerative diseases. While urea is believed to weaken the hydrophobic effect, a picture consistent with the decrease in the excess chemical potential of sufficiently large alkanes, interactions with protein polar side chains and backbone atoms are also important. Here, we study, through molecular dynamics, the hydration and aggregation of several alkanes and amphiphilic "mutants" of n-dodecane, in an 8M aqueous urea solution, aiming at getting insight into urea's mode of action. A size-dependent crossover temperature is found, above which the hydration of the alkanes is favored in the aqueous urea solution. The hydration of the alkanes is enhanced via entropy, with the enthalpy opposing hydration, consistent with experiments. The reason is that although solute-solvent interactions are favorable, these are overwhelmed by urea-water and urea-urea interactions. In contrast, water-water interactions and entropy are favored by a water depletion around the solute and a reduced water depletion around methane explains its exceptional solubility decrease. Furthermore, we show that while urea favors the hydration of n-dodecane and the amphiphilic mutants, it slightly enhances and reduces, respectively, the aggregation of the alkanes and the amphiphilic mutants. Thus, opposite to the common view, our results show that urea does not necessarily weaken hydrophobic interactions despite solvation being favored.

Molecular features of the interaction and antimicrobial activity of chitosan in a solution containing sodium dodecyl sulfate

Molecular interaction of chitosan with sodium dodecyl sulfate (SDS) is a more complicated process than it has been imagined so far. For the first time it has been shown that the shorter chitosan chains are, the more preferably they interact with the SDS and the larger-in-size microparticles they form. The influence of ionic strength, urea and temperature on microparticles formation allows interpreting the mechanism of microparticles formation as a cooperative electrostatic interaction between SDS and chitosan with simultaneous decrease in the surface charge of the complexes initiating the aggregation of microparticles. It is shown that hydrogen bonding is mainly responsible for the aggregation while hydrophobic interaction has a lesser effect. Chitosan demonstrates a high bacteriostatic activity in the presence of SDS in solution and can be promising for preparation of microbiologically stable pharmaceutical hydrocolloids, cosmetic products and chitosan-based Pickering emulsions containing strong anionic surfactants.

Breakdown of classical paradigms in relation to membrane structure and functions

Updates of the mosaic fluid membrane model implicitly sustain the paradigms that bilayers are closed systems conserving a state of fluidity and behaving as a dielectric slab. All of them are a consequence of disregarding water as part of the membrane structure and its essential role in the thermodynamics and kinetics of membrane response to bioeffectors. A correlation of the thermodynamic properties with the structural features of water makes possible to introduce the lipid membrane as a responsive structure due to the relaxation of water rearrangements in the kinetics of bioeffectors' interactions. This analysis concludes that the lipid membranes are open systems and, according to thermodynamic of irreversible formalism, bilayers and monolayers can be reasonable compared under controlled conditions. The inclusion of water in the complex structure makes feasible to reconsider the concept of dielectric slab and fluidity.

Mitigating effects of osmolytes on the interactions between nanoparticles and supported lipid bilayer

To maintain osmotic balance, cells usually produce neutral solutes (i.e., osmolytes), together with charged species to cope with salinity stress. Osmolytes are known to be important in stabilizing/destabilizing macromolecules (e.g., proteins) via depletion /accumulation around their surfaces. To better understand the physiological fate of nanoparticles (NPs), we investigated the effect of osmolytes [(urea and trimethylamine N-oxide (TMAO)] and specific anions (NO₃^- and F^-) on the interactions between NPs and supported lipid bilayers (SLBs). Carboxylated polystyrene NPs (60 nm) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) were chosen as model NPs and lipid. Quartz crystal microbalance with dissipation monitoring (QCM-D) was used to quantify NP deposition dynamics. Microscale thermophoresis (MST) was used to characterize the affinity between DOPC vesicles (or NPs) and osmolytes. Our results show that osmolytes are capable of protecting SLBs from NP-induced disruption. Upon NP deposition onto supported vesicle layers (SVLs), the leakage of encapsulated dyes decreased with the addition of osmolytes. The combination of kosmotropes (TMAO and F^-) are more efficient than that of chaotropes (urea and NO₃^-) in weakening the hydrophobic interaction between NPs and SLBs by preferential binding to NPs and/or SLBs.

Similar structural stabilities of 3-isopropylmalate dehydrogenases from the obligatory piezophilic bacterium Shewanella benthica strain DB21MT-2 and its atmospheric congener S. oneidensis strain MR-1

We previously found that the enzymatic activity of 3-isopropylmalate dehydrogenase from the obligatory piezophilic bacterium Shewanella benthica strain DB21MT-2 (SbIPMDH) was pressure-tolerant up to 100 MPa, but that from its atmospheric congener S. oneidensis strain MR-1 (SoIPMDH) was pressure-sensitive. Such characteristics were determined by only one amino acid residue at position 266, serine (SoIPMDH) or alanine (SbIPMDH) [Y. Hamajima et al. Extremophiles 20: 177, 2016]. In this study, we investigated the structural stability of these enzymes. At pH 7.6, SoIPMDH was slightly more stable against hydrostatic pressure than SbIPMDH, contrary to the physiological pressures of their normal environments. Pressure unfolding of these IPMDHs followed a two-state unfolding model between a native dimer and two unfolded monomers, and the dimer structure was pressure-tolerant up to 200 MPa, employing a midpoint pressure of 245.3 ± 0.1 MPa and a volume change of -225 ± 24 mL mol^-1 for the most unstable mutant, SbIPMDH A266S. Thus, their pressure-dependent activity did not originate from structural perturbations such as unfolding or dimer dissociation. Conversely, urea-induced unfolding of these IPMDHs followed a three-state unfolding model, including a dimer intermediate. Interestingly, the first transition was strongly pH-dependent but pressure-independent; however, the second transition showed the opposite pattern. Obtained volume changes due to urea-induced unfolding were almost equal for both IPMDHs, approximately +10 and -30 mL mol^-1 for intermediate formation and dimer dissociation, respectively. These results indicated that both IPMDHs have similar structural stability, and a pressure-adaptation mechanism was provided for only the enzymatic activity of SbIPMDH.

Injectable Shear-Thinning Fluorescent Hydrogel Formed by Cellulose Nanocrystals and Graphene Quantum Dots

In the search for new building blocks of nanofibrillar hydrogels, cellulose nanocrystals (CNCs) have attracted great interest because of their sustainability, biocompatibility, ease of surface functionalization, and mechanical strength. Making these hydrogels fluorescent extends the range of their applications in tissue engineering, bioimaging, and biosensing. We report the preparation and properties of a multifunctional hydrogel formed by CNCs and graphene quantum dots (GQDs). We show that although CNCs and GQDs are both negatively charged, hydrogen bonding and hydrophobic interactions overcome the electrostatic repulsion between these nanoparticles and yield a physically cross-linked hydrogel with tunable mechanical properties. Owing to their shear-thinning behavior, the CNC-GQD hydrogels were used as an injectable material in 3D printing. The hydrogels were fluorescent and had an anisotropic nanofibrillar structure. The combination of these advantageous properties makes this hybrid hydrogel a promising material and fosters the development of new manufacturing methods such as 3D printing.

Effects of the protein denaturant guanidinium chloride on aqueous hydrophobic contact-pair interactions

Guanidinium chloride (GdmCl) is one of the most common protein denaturants. Although GdmCl is well known in the field of protein folding, the mechanism by which it denatures proteins is not well understood. In fact, there are few studies looking at its effects on hydrophobic interactions. In this work the effect of GdmCl on hydrophobic interactions has been studied by observing how the denaturant influences model systems of phenyl and alkyl hydrophobic contact pairs. Contact pair formation is monitored through the use of fluorescence spectroscopy, i.e., measuring the intrinsic phenol fluorescence being quenched by carboxylate ions. Hydrophobic interactions are isolated from other interactions through a previously developed methodology. The results show that GdmCl does not significantly affect hydrophobic interactions between small moieties such as methyl groups and phenol; while on the other hand, the interaction of larger hydrophobes such as hexyl and heptyl groups with phenol is significantly destabilized.