Negative Charge Density Research Articles

A key piece of the puzzle: The central tetramer of the Saccharomyces cerevisiae septin protofilament and its implications for self-assembly

Septins, often described as the fourth component of the cytoskeleton, are structural proteins found in a vast variety of living beings. They are related to small GTPases and thus, generally, present GTPase activity which may play an important (although incompletely understood) role in their organization and function. Septins polymerize into long non-polar filaments, in which each subunit interacts with two others by alternating interfaces, NC and G. In Saccharomyces cerevisiae four septins are organized in the following manner, [Cdc11-Cdc12-Cdc3-Cdc10-Cdc10-Cdc3-Cdc12-Cdc11]n in order to form filaments. Although septins were originally discovered in yeast and much is known regarding their biochemistry and function, only limited structural information about them is currently available. Here we present crystal structures of Cdc3/Cdc10 which provide the first view of the physiological interfaces formed by yeast septins. The G-interface has properties which place it in between that formed by SEPT2/SEPT6 and SEPT7/SEPT3 in human filaments. Switch I from Cdc10 contributes significantly to the interface, whereas in Cdc3 it is largely disorded. However, the significant negative charge density of the latter suggests it may have a unique role. At the NC-interface, we describe an elegant means by which the sidechain of a glutamine from helix α0 imitates a peptide group in order to retain hydrogen-bond continuity at the kink between helices α5 and α6 in the neighbouring subunit, thereby justifying the conservation of the helical distortion. Its absence from Cdc11, along with this structure’s other unusual features are critically discussed by comparison with Cdc3 and Cdc10.

A serendipity of nanofiltration membrane modification using a simple approach: Limited sulfonamidation, remarkable improvements

Surface modification via secondary interfacial polymerization (IP) is a promising technology for the enhancement of nanofiltration (NF) membrane performance such as rejection selectivity. In this study, sulfuryl chloride (SC), containing sulfur element, was employed to introduce sulfonic groups into the active layer of membranes, with a main purpose of investigating the secondary IP mechanisms as well as the variation of membrane structural and physicochemical properties. Moreover, the SC-modified membranes would be endowed with favorable performance. Results showed that SC in a hexane environment behaved similarly with small and reactive diacyl dichloride in enhancing membrane surface negative charge density and contracting membrane pores. Membrane surface characterization showed that the sulfur element had a low concentration with an S/N ratio less than 0.04. This indicated that, on the one hand, the residual amine groups in the nascent active layer for secondary IP were quite limited, and on the other hand, the improvement of membrane performance was remarkably affected by the introduced sulfonyl groups. Consequently, SC in the hexane environment could further enhance the crosslinking degree of the active layer. In addition, SC modification could increase the membrane surface hydrophilicity and narrow the pore size distribution. The SC-modified membranes would be suitable for advanced treatment of drinking water. An optimized membrane with SC modification had a molecular weight cutoff of ∼350 Da and a surface zeta potential of ∼−55.8 mV, and could effectively reject five negatively charged per- and polyfluoroalkyl substances (with molecular weight ranging from 214 to 414 Da) by over 80% while with a low rejection of MgCl2 below 30%..

Assessment of Two Materials as Adsorbents for the Effective Removal and Further Pre-Concentration of Gallium from Aqueous Solutions: Mesoporous Carbon vs. Clinoptilolite

In this research, the adsorption of gallium onto natural zeolite (clinoptilolite) and two mesoporous-activated carbons were compared and evaluated. The clinoptilolite was treated with HCl (HCPL), while mesoporous-activated carbons (MCSG60A and MCO1) were synthesized by replica method, using sucrose as the carbon precursor and silica gel as the template. These carbonaceous materials showed large pore sizes and mesoporous surface, as well as a suitable surface chemistry for cation adsorption, which promotes a high negative charge density. On the other hand, zeolites have narrower pore sizes, which hinders the material diffusion inside the particle; however, its strength is their ion exchange capacity. Regarding the gallium kinetic studies, it is described by Pseudo-second order model for both sorts of adsorbents. MCO1 is the best carbonaceous adsorbent studied, with a capacity of 4.58 mg/g. As for zeolites, between the two zeolites studied, HCPL showed the best results, with a gallium adsorption capacity of 3.1 mg/g. The gallium adsorption mechanism onto MCO1 material is based on physisorption, while HCPL is mainly retained due to an ion-exchange process. Regarding the Giles classification, MCO1 isotherm described an H-4 pattern of high affinity and characteristic of multilayer adsorption. The Double-Langmuir model fits properly within these experimental results. In the case of zeolites, HCPL adsorption isotherm followed an L-2 pattern, typical of monolayer adsorption—the Sips model is the one that better describes the adsorption of gallium onto the zeolite.

Comparative analysis of gate structure dependent FET-based biosensor

In this work, four biosensors with different gate structures based on MOSFETs are examined. A conventional back gate and three different front gate-based structures are assessed in terms of change in the electrical parameters of transfer characteristics and sensitivity. Most importantly, all four structures are analyzed to consider the realistic process of biomolecule detection with varying fill-in factors of biomolecules, and sensitivity is calculated between the anti-iris antibody (bio target) and iris-antigen (bioreceptor). In a back-gate structure, the electrical parameter is only affected by the negative charge density of biomolecules which limits this topology to detect the neutral biomolecules, while in front-gate-based structures, the electrical parameters are affected by both dielectric permittivity and negative charge density; thus, front-gate-based biosensor structures show the applicability to detect the charged as well neutral biomolecules. The front gate single cavity and front gate mid cavity show the highest sensitivity for all the combinations of fill-in factors. This comparative study of different gate structures for varying fill-in factors on different locations of biomolecules in the cavity or sensing region proposes the guidelines for making suitable choices for MOSFET-based biosensor development.

Effect of cholesterol on the ion-membrane interaction: Zeta potential and dynamic light scattering study

Cholesterol in a bio-membrane plays a significant role in many cellular event and is known to regulate the functional activity of protein and ion channel. In this study we report a significant effect of cholesterol on the ion-membrane interaction. We prepare large unilamellar vesicles, composed of zwitterionic lipid DOPC and anionic lipid DOPG with different cholesterol concentration. Electrostatics of anionic membranes containing cholesterol in the presence of NaCl has systematically been explored using dynamic light scattering and zeta potential. Negative zeta potential of the membrane decreases its negative value with increasing ion concentration for all cholesterol concentrations. However, zeta potential itself decreases with increasing cholesterol content even in the absence of monovalent ions. Electrostatic behaviour of the membrane is determined from well-known Gouy Chapmann model. Negative surface charge density of the membrane decreases with increasing cholesterol content. Binding constant, estimated from the electrostatic double layer theory, is found to increase significantly in the presence of cholesterol. Comparison of electrostatic parameters of the membrane in the presence and absence of cholesterol suggests that cholesterol significantly alter the electrostatic behaviour of the membrane.

Influence mechanisms of epoxy degradation on surface traps and charge accumulation under DC electrical–thermal stress

As trapping sites for surface charges, the surface trap is an important factor affecting the insulation performance of the epoxy–SF6 interface, which is closely related to the microstructure and its evolution. However, existing studies often ignore the effect of the degradation of the epoxy surface on the surface traps and charge accumulation during the long-term service of the insulation system. In this study, the surface physicochemical evolution and its influence on surface traps of a typical epoxy–SF6 insulation structure were researched under a DC-temperature gradient condition, and an evolution mechanism of surface traps was proposed. The results show that the free radicals introduced during the material degradation process increase the density and depth of both positive and negative charge traps on the epoxy surface. The effect of free radicals formed by the cleavage of epoxy molecules on the electronic orbital and molecular electrostatic potential of epoxy molecules is the intrinsic reason for the evolution of surface trap evolution. This work may help to understand the long-term evolution mechanisms of the physicochemical characteristics of the epoxy–SF6 interface in DC field and may provide a theoretical basis for the long-term failure mechanism revealing and the insulation performance enhancement.

Purification and characterisation of heparin-like sulfated polysaccharides with potent anti-SARS-CoV-2 activity from snail mucus of Achatina fulica

Heparin-like sulfated polysaccharide, acharan sulfate, was purified from the mucus of an African giant snail with unique sulfated glycosaminoglycans (GAGs). This study reported on finding novel and safe heparin resources from Achatina fulica for further use as well as easy isolation and purification of the active fraction from the initial raw material. Its structure was characterised by a strong-anion exchange combined with high-performance liquid chromatography (HPLC) and nuclear magnetic resonance (NMR) spectroscopy. The results indicated that the potential acharan sulfate fraction is a glycosaminoglycan composed of several repeating disaccharide units, namely, of →4)−α−IdoA(2S)(1→4)−α−GlcNAc/GlcNAc(6S)/GlcNSO3(6S)(1→, and hence, presents heterogeneity regarding negative net charge density. Furthermore, the heparinase digests inhibit the binding of SARS-CoV-2 spike protein to the ACE2 receptor. In summary, the acharan sulfate presented in this work has shown its great potential for application in the preparation of sulfated polysaccharides as an alternative to heparin with important biological activity.

An experimental investigation on the impact of divalent ions on the emulsification of oil: Comparison of biodegradable (green) and petroleum-based surfactants

Emulsification of oil with surfactants often yields in complex colloidal systems which require understanding their physicochemical properties prior to their use in industry. This study aims to investigate the effects of divalent ions (calcium and magnesium) on the emulsification performance of biodegradable (green) surfactants of Triton™ CG-110 (alkyl polyglycoside, APG) and GreenZyme (GZ) at two temperature conditions (25 °C and 70 °C). For this purpose, the phase behaviour, interfacial tension (IFT), stability, droplet size distribution and rheological properties of APG and GZ microemulsion were evaluated. The outcomes were then compared with the emulsification performance of petroleum-based (synthetic) surfactants of alpha-olefin sulfonate (AOS) and cetyltrimethylammonium bromide (CTAB). Furthermore, the impacts of alkalis (ethanolamine and sodium carbonate) on microemulsions and the demulsification performance of a zwitterionic demulsifier (cocobetaine) were explored. The results show that only APG and CTAB could produce water in oil (W/O) microemulsions in the presence of divalent ions. The stability of APG and CTAB microemulsions was affected by divalent ions since the water segregation rate (WSR) index of these microemulsions went up from ≈21% to ≈ 85% as salinity increased up to 15 wt%. Also, the average droplet size of these microemulsions went up from 50-64 nm to 220–255 nm as salinity increased to 9 wt%. This is because the negative charge density on the microemulsion droplet surface decreases as the salinity increases, thus the electrostatic repulsive force between the droplets becomes weaker. In addition, APG and CTAB microemulsions showed a shear thinning behaviour, and their viscosity value increased with the increase in salinity. It is speculated that the presence of divalent ions generates more friction between the molecules, which causes an increase in the viscosity of the microemulsions.

Structural basis for the cold activation and adaptation of an α-agarase from marine bacterium Catenovulum agarivorans STB13

Enzymes have high activity at low temperatures are defined as cold-adapted enzymes, but few enzymes show an activation effect after low-temperature incubation. In this study, we cloned an agarase from the marine bacterium Catenovulum agarivorans STB13 (Ca-AGA) and expressed the protein in Bacillus subtilis. The enzyme exhibited a peculiar cold activation, which was enhanced by 5-fold after incubation at −20 °C or 4 °C for 6 h. Fluorescence and CD spectra studies confirmed the secondary and tertiary structural changes in Ca-AGA at low temperature, which formed compact protein structures after low-temperature treatment. The enzyme also showed outstanding cold adaptation, retaining approximately 60% of its maximum activity at 10 °C. Based on a bioinformatics analysis, the carbohydrate-binding modules (CBMs) and long linker region were presumed to play a crucial role in cold adaptation due to a relatively high percentage of acidic residues and a negative charge density compared to the catalytic domain. A mutation that truncated the linker-CBM region resulted in a 59.97% reduction of the activity at 10 °C. This study describes an α-agarase of cold activation and adaptation in detail, which may have great potential for producing functional agaro-oligosaccharides in food and pharmaceutical industrial applications at ambient temperature.

Electro-osmotic flow in different phosphorus nanochannels

The electrokinetic transport in a neutral system consists of an aqueous NaCl solution confined in a nanochannel with two similar parallel phosphorene walls and is investigated for different black, blue, red, and green phosphorene allotropes in the presence of an external electric field in the directions x (parallel to the walls roughness axis) and y (perpendicular to the walls roughness axis). The results show that irrespective of the electric field direction, the thickness of the Stern layer increases with the increase in the magnitude of the negative electric surface charge density (ESCD) on the nanochannel walls, and it also increases with the increase in the roughness ratio for different allotropes. Moreover, three different regimes of Debye–Hückel (DH), intermediate, and flow reversal appear as the absolute value of the negative ESCD on the walls grows. With the increase in the absolute value of the negative ESCD, in the DH regime, the flow velocity grows, then in the intermediate regime, it decreases, and finally, at sufficiently high ESCD, the flow reversal occurs. When the external electric field is applied in the y direction, the dynamics of the system are slower than that of the x direction; therefore, the flow reversal occurs at the smaller absolute values of the negative ESCD.

Understanding the Inhibition Mechanism of Lignin Adsorption to Cellulase in Terms of Changes in Composition and Conformation of Free Enzymes

The adsorption of lignin to cellulase is the major obstacle in the sugar-platform conversion of lignocellulosic bioresources. In this study, the adsorption behavior of untreated and pretreated lignin samples from corn stover to cellulase was investigated, in particular the effects of lignin adsorption on the composition and spatial conformation of free enzymes were explored. The results showed that pretreatments decreased the hydrophobic groups contents of lignin, i.e., aromatic ring, ether and carbonyl, as well as the content of ionizable group, i.e., carboxyl, which reduced its hydrophobicity and negative charge density, thus weakening the adsorption ability of lignin to cellulase. The lignin samples mainly adsorbed the CBHII component of cellulase to inhibit the synergistic effect of free enzymes. Lignin adsorption altered the spatial position of tryptophan residues in free enzymes, exposing them to the protein surface. In addition, the secondary structure of free enzymes was altered, with a decrease in the alpha-helix content and an increase in the random coil content, thus loosening the spatial conformation of free enzymes. The change degree in the spatial structure of free enzymes correlated with the adsorption capacity of the lignin, i.e., lignin with low adsorption capacity caused the least damage to free enzyme, with NaOH pretreated lignin being the best. It appears that appropriate pretreatment and chemical modification of enzymes to resist lignin adsorption is a promising long-term pathway to overcome the lignin inhibition during sugar-platform conversion of lignocellulosic bioresources.

Fluorenone-based covalent organic frameworks with efficient exciton dissociation and well-defined active center for remarkable photocatalytic hydrogen evolution

Precisely modulating both the fine structures and exciton behaviors of covalent organic framework (COF)-based photocatalysts for efficient photocatalytic hydrogen evolution is still a great challenge. Herein, we report two COFs, fluorenone-based COF (FOO-COF) and fluorenyl-based COF (FO-COF), for photocatalytic H2 evolution. The results demonstrated that FOO-COF achieved a remarkable stability and hydrogen evolution rate of 119.1 mmol/h/g, surpassing those of many previously reported COF-based photocatalysts, thus resulting in an apparent quantum efficiency up to 20.5% at 435 nm. The joint observations from temperature-dependent photoluminescence, the delayed fluorescence and phosphorescence spectroscopy confirm that FOO-COF shows a stronger carrier separation and migration ability, much lower exciton binding energy, and faster dissociation speed of singlet and triplet excitons than FO-COF. More importantly, the femtosecond time-resolved transient absorption spectra (fs-TAS) revealed the great difference between the two COFs in electron trapping and exciton dissociation after Pt loading. Furthermore, theoretical calculations unveiled the feasibility of CO groups in the LUMO sites of FOO-COF as active electronic centers for anchoring the photodeposited Pt cocatalysts, due to its much lower Gibbs free energy of hydrogen adsorption and more negative charge density. We believe that the introduction of CO groups in the FOO-COF can act as both a dominant electronic collection center and partial active sites, which improve the D-A polarizability and boost the generation, separation, migration, and utilization of photogenerated carriers in the FOO-COF for achieving remarkable photocatalytic hydrogen evolution. The insights into the molecular-level mechanism in this work may guide the significance of the rational design of COF structures for advanced photocatalytic hydrogen evolution.

Potential risk resulting from the influence of static magnetic field upon living organisms. Numerically simulated effects of the static magnetic field upon fatty acids and their glycerides

Background: We attempt to recognise the effects of static magnetic field (SMF) of varying flux density on flora and fauna. For this purpose, the influence of static magnetic field is studied for molecules of octadecanoic (stearic), cis-octadec-9-enoic (oleic), cis,cis-octadec-9,12-dienoic (linoleic), all cis-octadec-6,9.12-trienoic (linolenic), trans-octadec-9-enoic – (elaidic), cis-octadec-11-enoic (vaccenic) and all trans-octadec-6,9,12-trienoic (trans-linolenic) acids as well as 1- and 2-caproyl monoglycerides, 1,2- and 1,3-caproyl diglycerides and 1,2,3-caproyl triglyceride. In such a manner we attempt to develop an understanding of the interactions of living cells with SMF on a molecular level. Methods: Computations of the effect of real SMF 0.0, 0.1, 1, 10 and 100 AMFU (Arbitrary Magnetic Field Unit; here 1AMFU > 1000 T) flux density were performed in silico (computer vacuum), involving advanced computational methods. Results: SMF polarises molecules depending on applied flux density It neither ionises nor breaks valence bonds at 0.1 and 1 AMFU. In some molecules under consideration flux density of 10 and 100AMFU some C-H and C-C bonds were broken. Some irregularities were observed in the changes of positive and negative charge densities and bond lengths against increasing flux density. They provide evidence that molecules slightly change their initially fixed positions with respect to the force lines of the magnetic field. The length of some bonds and bond angles change with an increase in the applied flux density providing, in some cases, polar interactions between atoms through space. Conclusions: SMF destabilizes lipid acids and caproyl glycerides irregularly against increasing flux density. That irregularity results from the ability of those molecules to twist out of the initially established SMF plain and squeeze molecules around some bonds. In some molecules SMF flux density of 10 AMFU and above breaks some valence bonds and only in case of elaidic acid the trans-cis conversion is observed. Depending on the structure and applied flux density SMF either stimulates or inhibits metabolic processes of the lipids under study.

Treatment of simulated saline brine water by membrane distillation process enhanced through alternating current electric field

Treatment of saline brine has been a tricky challenge in recent years, and membrane distillation (MD) is considered as a promising alternative technology. But it was found that the normalized flux significantly decreased to 0.6 within 15 h when treating simulated salinity brine, which was caused by the deposition of the humic acids (HA), CaSO4, and HA-Ca complex, suggesting the severe membrane fouling. In this study, a composite membrane was fabricated by coating carbon nanotubes (CNT) on the commercial PTFE membrane, and an alternating current (AC) electric field was subsequently applied that aimed to improve MD performance. Specially, the application of 50 Hz square wave dramatically retarded the inorganic fouling and the intensity of membrane organic matter was reduced by 60.6% due to its hydrophilic surface and instantaneous polarity conversion, thus its normalized flux even maintained around 0.9 after 15 h operation. Coupled with the modified XDLVO analysis, the coating CNT layer exhibited good resistance of HA due to their electrostatic repulsions, both of which carried a strong negative charge and high density hydrophilic functional groups. It was also found that except the movement distance of charged substances far greater than the thickness of the fixed electrostatic double layer, AC electric field with certain frequency significantly reduced the coexistence time for substances with opposite charge by keeping them in motion that could further alleviate the fouling. This study suggested that a hybrid system of AC electric field and MD would provide a potential alternative for treating the salinity brine water.

Synergistic effects of Gemini cationic surfactants with multiple quaternary ammonium groups and anionic surfactants with long EO chains in the mixed systems

In this study, two different anionic surfactants containing long polyoxyethylene chains involving sodium fatty alcohol ether carboxylates (AE9C) as well as isomeric sodium fatty alcohol ether sulfates (iso-AE9S) are mixed with a new Gemini cationic surfactant bearing four quaternary ammonium groups (TC-GS). Then, the surface properties and aggregation behavior of the two mixed systems were investigated. The effect of the long polyoxyethylene chains on the conformation and hydration of the hydrophilic head group of AE9C and iso-AE9S weakened their negative charge density, thus hindering their excessive electrostatic adsorption with TC-GS and improving the stability of the mixed systems. The positive synergistic effects of TC-GS/AE9C and TC-GS/iso-AE9S exhibited significantly lower critical micelle concentration, faster diffusion rates, and superior wetting capability compared to single surfactants. The micellization process of both mixed systems is spontaneously enthalpy-driven, and the diffusion-adsorption process is consistent with the mixed diffusion-kinetic mechanism. Finally, both mixed systems are capable of forming complex and interesting aggregate morphologies, with TC-GS/AE9C can form multilayer spherical vesicles and TC-GS/iso-AE9S can form multicompartment concentric spherical vesicles.

Changes in molybdenum bioaccessibility in four spiked soils with respect to soil pH and organic matter

Investigation of the inherent relationship between soil physicochemical properties and pollutant's bioaccessibility (BAc) by analyzing different soil types may produce erroneous results or bias, owing to the complexity of natural soil characteristics. However, use of single factor analysis (e.g., soil pH, organic matter) facilitates evaluation of the transition. In this study, the inherent relationship between soil properties and the BAc of molybdenum (Mo) was evaluated in two typical variable-charge soils (Ferralosol and Ferrosol) and constant-charge soils (Alfisol and Inceptisol) spiked with Mo after adjusting their pH and organic carbon content. The Unified Bioaccessibility Research Group of Europe (BARGE) Method (UBM) was applied to evaluate the BAc of Mo in the gastric and intestinal phase (GP and IP, respectively). Isothermal adsorption experiment, Tessier sequential extraction, and field emission scanning electron microscope-energy dispersive spectroscopy (FESEM-EDS) analysis were conducted on these spiked soils. The results indicated that the BAc of Mo in IP (27.42–80.41%) was significantly higher than that in GP (2.52–28.53%). A significantly lower level of BAc of Mo was found in the variable-charge soils, when compared with that in the constant-charge soils. Furthermore, significant negative correlations were identified between the BAc and adsorption of Mo, which decreased with soil pH. These negative correlations can be attributed to the increase in soil negative charge density and enhancement of Mo desorption by hydroxyl, which reinforce the repulsion between Mo and soil particles with increasing soil pH; this was further confirmed by the decrease in Mo adsorption with Alfisol pH. The Mo fractions and FESEM-EDS patterns confirmed that the BAc of Mo in GP was negatively correlated with soil organic carbon (SOC) content, possibly owing to an increase in Mo retention by SOC. These findings indicated that the health risk of Mo contamination in low pH and SOC-rich variable-charge soil is relatively low, thus providing references for rationalizing risk assessment and remediating Mo-polluted soil.

Enhanced activity of Fe/Mn nanoparticles using a response surface methodology and mechanism for removing oxytetracycline and copper ion

As feed additives, oxytetracycline (OTC) and copper ion (Cu(II)) are often detected in livestock and poultry farming wastewater. To address this issue, firstly, the synthesis conditions of Fe/Mn nanoparticles (Fe/Mn NPs) were initially optimized using a response surface methodology (RSM) to yield highly active Fe/Mn NPs, where the application of RSM significantly increased the Fe/Mn NPs’ efficiency in removing co-contamination OTC and Cu(II),respectively, from 45.8 to 86.2% and 14.9–67.2%. Secondly, scanning electron microscope and Nitrogen adsorption-desorption isotherms results showed that Fe/Mn NPs were composed of elliptic particles between 20 and 40 nm, a specific surface area of 59.5 m2 g−1, and a mean pore diameter of 5.27 nm. Fourier infrared spectrometer and X-ray photoelectron spectroscopy analysis revealed that amino, carboxyl and hydroxyl functional groups existed on the surface. Zeta potential indicated that Fe/Mn NPs maintained a high negative charge density between pH 1 and 11. These surface properties possessed by the green synthesized Fe/Mn NPs resulted in high adsorption efficiency for co-contamination OTC and Cu(II). Based on this, a removal mechanism based on a combination of complex-bridging effect, pore-filling, hydrogen bonding, surface complexation, ion exchange and electrostatic attraction was proposed. Finally, the assessment of Fe/Mn NPs used in swine wastewater demonstrated that both 99.9% OTC and 55.6% Cu(II) were removed.

Reductionist insights into how chaperone charge influences RNA folding.

Non-coding RNAs are composed of modular secondary and tertiary structural units that themselves must form complex 3D structures for the entire RNA to fold and perform its biological function. However, the high density of negative charges associated with the phosphate backbone gives rise to substantial amounts of electrostatic repulsion, contributing to the large energetic barrier between unfolded and folded states. RNA folding chaperones (RFCs) are proteins that help lower this energy barrier by transiently interacting with RNA. Recent work has shown that some RFCs can function as macromolecular counterions for their RNA clients, thereby screening backbone electrostatic repulsion. However, the fundamental principles associated with how RFCs assist folding is largely unexplored. Here, we reduce RFCs to their smallest cationic constituents and then systematically “re-build” RFCs from these components (e.g., NH4+→ Lys→ polyK10→ RFC). We use single-molecule FRET to determine how these counterions influence both the relative population abundance and mean FRET efficiency of the folded and unfolded states of small model RNAs. From these studies, we have begun to determine aspects of RFCs that contribute to chaperoning RNA folding, such as net cationic charge and charge distribution. Here, we show that cationic amino acids (e.g., Lys and Arg) bind to RNA with apparent Kd values (appKd) on the order of 100 mM, which are comparable to those associated with their characteristic functional groups (e.g., ammonium and guanidinium). Further, increasing the net cationic charge of a counterion systematically decreases the appKd over several orders of magnitude. We also show a correlation between the decrease in appKd and a decrease in the folding free energy barrier. We then compare our observations of these polypeptide chaperones to the behavior of known RFCs (e.g., protamine, H1, and HCV nucleocapsid protein) with the small model RNAs.

Molecular fingerprint in hyaluronan-peptide interactions: Cooperation of electrostatics and side-chain specificity in enhanced arginine effect.

Hyaluronan is a sugar polymer found on the extracellular side, close to the plasma membrane. It is the scaffold of the extracellular matrix due to its high solubility, despite its low negative charge density and unusual length. Hyaluronan is also a known ligand of several glycan-binding proteins. We can improve our understanding of these interactions by characterizing hyaluronan affinity to model amino acid sequences of reduced complexity. Extracted features and fingerprints allow for identifying new potential binding partners and expand the current understanding of hyaluronan's biological role. Here, we use a combination of NMR and molecular dynamics simulations (MD) to study hyaluronan binding to short oligopeptides. We focus on arginine as a known critical amino acid for this interaction and compare it to lysine and glycine to highlight its distinctive features. We can test the binding using 1H NMR chemical shift perturbation (CSP) by titrating hyaluronan with a peptide. CSP not only estimates binding strength but also pinpoints the binding motif involved. Our findings are further explained by MD, which provide an atomistic fingerprint of the hyaluronan-peptide complex. Interestingly, we could not find any NOE signal confirming the CSP observed interactions. The combination of positive CSP with no visible NOEs indicates the presence of a dynamic binding mode in agreement with our MD simulations. This agreement with simulations was only achieved using the prosECCo force field for accounting for electronic polarizability. Overall, we find that arginine, a positively charged amino acid, binds the strongest to the negative hyaluronan, followed by the positive lysine. The hyaluronan's carboxyl and amide groups are the driving force for interacting with the peptides. We prove the importance of the electrostatics interaction but also a specific sidechain affinity that favors arginine.

Fine-Tuning the Degree of Negative Charge and Carboxylate Grafting Density of Polymer-Coated Magnetite Nanoparticle

The surface of magnetite nanoparticle (MNP) was modified with poly(acrylic acid)(PAA)-poly(ethylene glycol) methyl methacrylate (PEGMA) (co)polymer to obtain water dispersible MNP with pH sensitive surfaces via atom transfer radical polymerization (ATRP) of tert-butyl acrylate (t-BA), followed by the t-BA group deprotection. Molar compositions of the (co)polymer were systematically varied, namely 100:0, 75:25, 50:50 and 25:75 of P(t-BA)/PEGMA, respectively, such that the grafting density of carboxylate groups on the MNP surface after the deprotection can be fine-tuned. Transmission electron microscopy (TEM) indicated that the MNP were spherical (ca.5-12 nm in diameter) with some nanoclustering observed. The roles of PAA and PEGMA affecting the hydrodynamic size and zeta potential of the nanocomposites observed via photocorrelation spectroscopy (PCS) were discussed. The percentages of the polymeric composition in the nanocomposites in each step of the reaction were determined via thermogravimetric analysis (TGA) and their magnetic properties were studied via vibrating sample magnetometry (VSM). These novel nanocomposites with pH sensitive surface and magnetically guidable properties might be advantageous for further conjugations either by covalent or ionic bonding with bioentities. HIGHLIGHTS Magnetite nanoparticle (MNP) coated poly(acrylic acid)(PAA)-poly(ethylene glycol) methyl methacrylate (PEGMA) (co)polymer were fabricated via ATRP The ratio of t-BA to PEGMA used in the copolymerization was studied The nanocomposites showed pH sensitive surface and magnetically guidable properties GRAPHICAL ABSTRACT