Studying salt effects on protein stability using ribonuclease t1 as a model system

Deciphering the Thermodynamic Landscape of CRISPR/Cas9: Insights into Enhancing Gene Editing Precision and Efficiency

The thermodynamic landscape of the CRISPR/Cas9 system plays a crucial role in understanding and optimizing the performance of this revolutionary genome-editing technology. In this research, we utilized isothermal titration calorimetry and microscale thermophoresis techniques to thoroughly investigate the thermodynamic properties governing CRISPR/Cas9 interactions. Our findings revealed that the binding between sgRNA and Cas9 is primarily governed by entropy, which compensates for an unfavorable enthalpy change. Conversely, the interaction between the CRISPR RNP complex and the target DNA is characterized by a favorable enthalpy change, offsetting an unfavorable entropy change. Notably, both interactions displayed negative heat capacity changes, indicative of potential hydration, ionization, or structural rearrangements. However, we noted that the involvement of water molecules and counterions in the interactions is minimal, suggesting that structural rearrangements play a significant role in influencing the binding thermodynamics. These results offer a nuanced understanding of the energetic contributions and structural dynamics underlying CRISPR-mediated gene editing. Such insights are invaluable for optimizing the efficiency and specificity of CRISPR-based genome editing applications, ultimately advancing our ability to precisely manipulate genetic material in various organisms for research, therapeutic, and biotechnological purposes.

Impact of Ultrafiltration on the Physicochemical Properties of Bovine Lactoferrin: Insights into Molecular Mass, Surface Morphology, and Elemental Composition

The large-scale isolation of bovine lactoferrin (bLF) typically involves using large amounts of concentrated eluents, which might introduce impurities to the final product. Sometimes, protein pre-concentration is required for the greater accuracy of experimental results. In this research, the supplied bLF sample was subjected to additional ultrafiltration (UF) to eliminate possible small impurities, such as salts and peptides of bLF. Beforehand, the basic characterization of native bLF, including surface-charge properties and the structural sensitivity to the various pH conditions, was performed. The study aimed to evaluate the difference in molecular mass, primary structure, surface morphology, and elemental composition of the protein before and after UF. The research was provided by application of spectroscopic, spectrometric, electrophoretic, and microscopic techniques. The evident changes in the surface morphology of bLF were observed after UF, while the molecular masses of both proteins were comparable. According to MALDI-TOF/MS results, UF had a positive impact on the bLF sample representation, improving the identification parameters, such as sequence coverage and intensity coverage.

Hydrogen-Deuterium Exchange Dynamics of NISTmAb Measured by Small Angle Neutron Scattering

Understanding protein dynamics and conformational stability holds great significance in biopharmaceutical research. Hydrogen-deuterium exchange (HDX) is a quantitative methodology used to examine these fundamental properties of proteins. HDX involves measuring the exchange of solvent-accessible hydrogens with deuterium, which yields valuable insights into conformational fluctuations and conformational stability. While mass spectrometry is commonly used to measure HDX on the peptide level, we explore a different approach using small-angle neutron scattering (SANS). In this work, SANS is demonstrated as a complementary and noninvasive HDX method (HDX-SANS). By assessing subtle changes in the tertiary and quaternary structure during the exchange process in deuterated buffer, along with the influence of added electrolytes on protein stability, SANS is validated as a complementary HDX technique. The HDX of a model therapeutic antibody, NISTmAb, an IgG1κ, is monitored by HDX-SANS over many hours using several different formulations, including salts from the Hofmeister series of anions, such as sodium perchlorate, sodium thiocyanate, and sodium sulfate. The impact of these formulation conditions on the thermal stability of NISTmAb is probed by differential scanning calorimetry. The more destabilizing salts led to heightened conformational dynamics in mAb solutions even at temperatures significantly below the denaturation point. HDX-SANS is demonstrated as a sensitive and noninvasive technique for quantifying HDX kinetics directly in mAb solution, providing novel information about mAb conformational fluctuations. Therefore, HDX-SANS holds promise as a potential tool for assessing protein stability in formulation.

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.

pH-dependent self-assembly mechanism of a single repetitive domain from a spider silk protein

Spider silk is self-assembled from full-length silk proteins, and some silk protein fragments can also form silk-like fibers in vitro. However, the mechanism underlying the silk fiber formation is not understood well. In this study, we investigated the fiber formation of a single repetitive domain (RP) from a minor ampullate silk protein (MiSp). Our findings revealed that pH and salt concentration affect not only the stability of MiSp-RP but also its self-assembly into fibers and aggregates. Using nuclear magnetic resonance (NMR) spectroscopy, we solved the three-dimensional (3D) structure of MiSp RP in aqueous solution. On the basis of the structure and mutagenesis, we revealed that charge-dipole interactions are responsible for the pH- and salt-dependent properties of MiSp-RP. Our results indicate that fiber formation is regulated by a delicate balance between intermolecular and intramolecular interactions, rather than by the protein stability alone. These findings have implications for the design of silk proteins for mass production of spider silk.

How a highly acidic SH3 domain folds in the absence of its charged peptide target

Charged residues on the surface of proteins are critical for both protein stability and interactions. However, many proteins contain binding regions with a high net-charge that may destabilize the protein but are useful for binding to oppositely charged targets. We hypothesized that these domains would be marginally stable, as electrostatic repulsion would compete with favorable hydrophobic collapse during folding. Furthermore, by increasing the salt concentration we predict that these protein folds would be stabilized by mimicking some of the favorable electrostatic interactions that take place during target binding. We varied the salt and urea concentrations to probe the contributions of electrostatic and hydrophobic interactions for the folding of the 60-residue yeast SH3 domain found in Abp1p. The SH3 domain was significantly stabilized with increased salt concentrations according to the Debye-Huckel limiting law. Molecular dynamics and NMR show that sodium ions interact with all 15 acidic residues but do little to change backbone dynamics or overall structure. Folding kinetics experiments show that the addition of urea or salt primarily affects the folding rate, indicating that almost all the hydrophobic collapse and electrostatic repulsion occurs in the transition state. After the transition state formation, modest yet favorable short-range salt-bridges are formed along with hydrogen bonds, as the native state fully folds. Thus, hydrophobic collapse offsets electrostatic repulsion to ensure this highly charged binding domain can still fold and be ready to bind to its charged peptide targets, a property that is likely evolutionarily conserved over one billion years.

Statement for broader audience

Some protein domains are highly charged because they are adapted to bind oppositely charged proteins and nucleic acids. However, it is unknown how these highly charged domains fold as during folding there will be significant repulsion between like-charges. We investigate how one of these highly charged domains folds in the presence of salt, which can screen the charge repulsion and make folding easier, allowing us to understand how folding occurs despite the protein’s high charge.

Supplementary material

Supplementary material document containing additional details on protein expression methods, thermodynamics and kinetics equations, and the effect of urea on electrostatic interactions, as well as 4 supplemental figures and 4 supplemental data tables. ( Supplementary_Material.docx ), 15 pages Supplemental excel file containing covariation data across AbpSH3 orthologs ( FileS1.xlsx ).

Hofmeister Effects of Group II Cations as Seen in the Unfolding of Ribonuclease A

This work studies the effects of alkaline-earth cation addition upon the unfolding free energy of a model protein, pancreatic Ribonuclease A (RNase A) by DSC analysis.  RNase A was chosen because it: a) does not specifically bind Mg 2+ , Ca 2+ and Sr 2+ cations and b) maintains its structural integrity throughout a large pH range. We have measured and compared the effects of NaCl, MgCl 2 , CaCl 2 and SrCl 2 addition on the melting point of RNase A.  Our results show that even though the addition of group II cations to aqueous solvent reduces the solubility of nonpolar residues (and enhances the hydrophobic effect), their interactions with the amide moieties are strong enough to "salt-them-in" the solvent, thereby causing an overall reduction in protein stability. We demonstrate that amide-cation interactions are a major contributor to the observed "Hofmeister Effects" of group II cations in protein folding. Our analysis suggests that protein folding "Hofmeister Effects" of group II cations, are mostly the aggregate sum of how cation addition simultaneously salts-out hydrophobic moieties through increasing the cavitation free energy, while promoting the salting-in of amide moieties through contact pair formation.

Nanopore Current Enhancements Lack Protein Charge Dependence and Elucidate Maximum Unfolding at Protein's Isoelectric Point

Protein sequencing, as well as protein fingerprinting, has gained tremendous attention in the electrical sensing realm of solid-state nanopores and is challenging due to fast translocations and the use of high molar electrolytes. Despite providing an appreciable signal-to-noise ratio, high electrolyte concentrations can have adverse effects on the native protein structure. Herein, we present a thorough investigation of low electrolyte sensing conditions across a broad pH and voltage range generating conductive pulses (CPs) irrespective of protein net charge. We used Cas9 as the model protein and demonstrated that unfolding is noncooperative, represented by the gradual elongation or stretching of the protein, and sensitive to both the applied voltage and pH (i.e., charge state). The magnitude of unfolding and the isoelectric point (pI) of Cas9 was found to be correlated and a critical factor in our experiments. Electroosmotic flow (EOF) was always aligned with the transit direction, whereas electrophoretic force (EPF) was either reinforcing (pH < pI) or opposing (pH > pI) the protein's movement, which led to slower translocations at higher pH values. Further exploration of higher pH values led to slowing down of protein with > 30% of the population being slower than 0.5 ms. Our results would be critical for protein sensing at very low electrolytes and to retard their translocation speed without resorting to high-bandwidth equipment.

Molecularly imprinted polypyrrole based sensor for the detection of SARS-CoV-2 spike glycoprotein

This study describes the application of a polypyrrole-based sensor for the determination of SARS-CoV-2-S spike glycoprotein. The SARS-CoV-2-S spike glycoprotein is a spike protein of the coronavirus SARS-CoV-2 that recently caused the worldwide spread of COVID-19 disease. This study is dedicated to the development of an electrochemical determination method based on the application of molecularly imprinted polymer technology. The electrochemical sensor was designed by molecular imprinting of polypyrrole (Ppy) with SARS-CoV-2-S spike glycoprotein (MIP-Ppy). The electrochemical sensors with MIP-Ppy and with polypyrrole without imprints (NIP-Ppy) layers were electrochemically deposited on a platinum electrode surface by a sequence of potential pulses. The performance of polymer layers was evaluated by pulsed amperometric detection. According to the obtained results, a sensor based on MIP-Ppy is more sensitive to the SARS-CoV-2-S spike glycoprotein than a sensor based on NIP-Ppy. Also, the results demonstrate that the MIP-Ppy layer is more selectively interacting with SARS-CoV-2-S glycoprotein than with bovine serum albumin. This proves that molecularly imprinted MIP-Ppy-based sensors can be applied for the detection of SARS-CoV-2 virus proteins.

Hofmeister effects on protein stability are dependent on the nature of the unfolded state

The interpretation of a salt's effect on protein stability traditionally discriminates low concentration regimes (<0.3 M), dominated by electrostatic forces, and high concentration regimes, generally described by ion-specific Hofmeister effects. However, increased theoretical and experimental studies have highlighted observations of the Hofmeister phenomena at concentration ranges as low as 0.001 M. Reasonable quantitative predictions of such observations have been successfully achieved throughout the inclusion of ion dispersion forces in classical electrostatic theories. This molecular description is also on the basis of quantitative estimates obtained resorting to surface/bulk solvent partition models developed for ion-specific Hofmeister effects. However, the latter are limited by the availability of reliable structures representative of the unfolded state. Here, we use myoglobin as a model to explore how ion-dependency on the nature of the unfolded state affects protein stability, combining spectroscopic techniques with molecular dynamic simulations. To this end, the thermal and chemical stability of myoglobin was assessed in the presence of three different salts (NaCl, (NH₄)₂SO₄ and Na₂SO₄), at physiologically relevant concentrations (0-0.3 M). We observed mild destabilization of the native state induced by each ion, attributed to unfavorable neutralization and hydrogen-bonding with the protein side-chains. Both effects, combined with binding of Na⁺, Cl^- and SO₄^2- to the thermally unfolded state, resulted in an overall destabilization of the protein. Contrastingly, ion binding was hindered in the chemically unfolded conformation, due to occupation of the binding sites by urea molecules. Such mechanistic action led to a lower degree of destabilization, promoting surface tension effects that stabilized myoglobin according to the Hofmeister series. Therefore, we demonstrate that Hofmeister effects on protein stability are modulated by the heterogeneous physico-chemical nature of the unfolded state. Altogether, our findings evidence the need to characterize the structure of the unfolded state when attempting to dissect the molecular mechanisms underlying the effects of salts on protein stability.

Molecular Mechanistic Insights into the Ionic-Strength-Controlled Interfacial Behavior of Proteins on a TiO2 Surface

By adjusting the ionic strengths through changing the concentration of the buffer ions, the molecular force and the interfacial behavior of cytochrome c (Cyt c) and TiO₂ are systematically studied. The molecular forces determined by combining the adhesion force and adsorption capacity are found to first increase and then decrease with the increasing ionic strength, with a peak obtained at an ionic strength between 0.8 and 1.0 M. The mechanism is explained based on the dissociation and hydration of ions at the interfaces, where the buffer ions could be completely dissociated at ionic strengths of <0.8 M but were partially associated when the ionic strength increased to a high value (>1.2 M), and the strongest hydration was observed around 1.0 M. The hydrodynamic size and the zeta potential value representing the effective contact area and protein stability of the Cyt c molecule, respectively, are also affected by the hydration and are proportional to the molecular forces. The interfacial behavior of Cyt c molecules on the TiO₂ surface, determined through surface-enhanced Raman scattering (SERS), is extremely affected by the ionic strength of the solution as the ion dissociation and hydration also increase the electron transfer ability, where the best SERS enhancement is observed at the ionic strength of around 1.0 M, corresponding to the largest molecular force. Our results provide a detailed understanding at the nanoscale on controlling the protein interfacial behavior with solid surfaces, adjusted by the buffer ions.

Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions

Liquid-liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.

Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions

Liquid-liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.

Improvement of sludge dewaterability by ammonium sulfate and the potential reuse of sludge as nitrogen fertilizer

A novel method to enhance sludge dewaterability with ammonium sulfate ((NH₄)₂SO₄) was proposed, and the potential reuse of dewatered sludge cake and filtrate as nitrogen fertilizers was evaluated. Compared with raw sludge, 87.91% reduction of capillary suction time (CST) and 88.02% reduction of specific resistance to filtration (SRF) after adding 80% (m/m) (NH₄)₂SO₄ were achieved, with 38.49% of protein precipitated simultaneously. The (NH₄)₂SO₄ dose destroyed cell membrane, resulting in the release of intracellular water by converting bound water into free water, thus enhancing sludge dewaterability. In the solid phase, the content of protein-N increased, and larger protein aggregates were formed. The (NH₄)₂SO₄ dose destroyed the hydration shell, making proteins to exhibit hydrophobic interactions, and to be aggregated, and precipitated from the liquid phase. When incubated Pennisetum alopecuroides L. with the dewatered sludge cake and filtrate after dewatering and conditioning with (NH₄)₂SO₄, the germination rate of grass seed and shoot lengths both increased while compared with those incubated with dewatered sludge cake and filtrate of the raw sludge. This study might provide insights into sustainable sludge treatment by integrating sludge dewatering and the potential reuse of dewatered sludge cake and filtrate as nitrogen fertilizer via treatment with (NH₄)₂SO₄.

De novo transcriptome analysis of Rhizophora mucronata Lam. furnishes evidence for the existence of glyoxalase system correlated to glutathione metabolic enzymes and glutathione regulated transporter in salt tolerant mangroves

The accumulation of a metabolic by product - methylglyoxal above a minimal range can be highly toxic in all organisms. Stress induced elevation in methylglyoxal inactivates proteins and nucleic acids. Glutathione dependent glyoxalase enzymes like glyoxalase I and glyoxalase II together with glutathione independent glyoxalase III play inevitable role in methylglyoxal detoxification. Glyoxalase genes are generally conserved but with obvious exceptions. Mangroves being potent harsh land inhabitants, their internal organelles are constantly been exposed to elevated levels of methylglyoxal. First and foremost it is important to detect the presence of glyoxalases in mangroves. De novo transcriptome analysis of mangrove species Rhizophora mucronata Lam., identified eleven putative glyoxalase proteins (RmGLYI-1 to 5, RmGLYII-1 to 5 and RmGLYIII). Molecular characterization proposed PLN02300 or PLN02367 as the key domains of RmGLYI proteins. They possess molecular weight ranging from 26.45 to 32.53 kDa and may localize in cytosol or chloroplast. RmGLYII proteins of molecular weight 28.64-36 kDa, carrying PLN02398 or PLN02469 domains are expected to be localized in diverse cellular compartments. Cytosolic RmGLYIII with DJ-1/PfpI domain carries a molecular weight 26.4 kDa. Detailed structural analysis revealed monomeric nature of RmGLYI-1 and RmGLYII-1 whereas RmGLYIII is found to be homodimer. Molecular phylogenetic analysis and multiple sequence alignment specified conserved metal ion/substrate binding residues of RmGLY proteins. Estimation of relative expression of glyoxalases under salt stress indicated the prominence of RmGLYI and RmGLYII over RmGLYIII. The aforementioned prominence is supported by salt induced expression difference of glutathione metabolic enzymes and glutathione regulated transporter protein.

Salt Dependence Conformational Stability of the Dimeric SAM Domain of MAPKKK Ste11 from Budding Yeast: A Native-State H/D Exchange NMR Study

The sterile α motif, also called the SAM domain, is known to form homo or heterocomplexes that modulate diverse biological functions through the regulation of specific protein-protein interactions. The MAPK pathway of budding yeast Saccharomyces cerevisiae is comprised of a three-tier kinase system akin to mammals. The MAPKKK Ste11 protein of yeast contains a homodimer SAM domain, which is critical for transmitting cues to the downstream kinases. The structural stability of the dimeric Ste11 SAM is maintained by hydrophobic and ionic interactions at the interfacial amino acids. The urea-induced equilibrium-unfolding process of the Ste11 SAM domain is cooperative without evidence of any intermediate states. The native-state H/D exchange under subdenaturing conditions is a useful method for the detection of intermediate states of proteins. In the present study, we investigated the effect of ionic strength on the conformational stability of the dimer using the H/D exchange experiments. The hydrogen exchange behavior of the Ste11 dimer under physiological salt concentrations reveals two partially unfolded metastable intermediate states, which may be generated by a sequential and cooperative unfolding of the five helices present in the domain. These intermediates appear to be significant for the reversible unfolding kinetics via hydrophobic collapse. In contrast, higher ionic concentrations eliminate this cooperative interactions that stabilize the pairs of helices.

Facile generation of giant unilamellar vesicles using polyacrylamide gels

Giant unilamellar vesicles (GUVs) are model cell-sized systems that have broad applications including drug delivery, analysis of membrane biophysics, and synthetic reconstitution of cellular machineries. Although numerous methods for the generation of free-floating GUVs have been established over the past few decades, only a fraction have successfully produced uniform vesicle populations both from charged lipids and in buffers of physiological ionic strength. In the method described here, we generate large numbers of free-floating GUVs through the rehydration of lipid films deposited on soft polyacrylamide (PAA) gels. We show that this technique produces high GUV concentrations for a range of lipid types, including charged ones, independently of the ionic strength of the buffer used. We demonstrate that the gentle hydration of PAA gels results in predominantly unilamellar vesicles, which is in contrast to comparable methods analyzed in this work. Unilamellarity is a defining feature of GUVs and the generation of uniform populations is key for many downstream applications. The PAA method is widely applicable and can be easily implemented with commonly utilized laboratory reagents, making it an appealing platform for the study of membrane biophysics.

Mechanistic Study of Protein Adsorption on Mesoporous TiO2 in Aqueous Buffer Solutions

Protein adsorption is of fundamental importance for bioseparation engineering applications. In this work, a series of mesoporous TiO₂ with various geometric structures and different aqueous buffer solutions were prepared as platforms to investigate the effects of the surface geometry and ionic strength on the protein adsorptive behavior. The surface geometry of the TiO₂ was found to play a dominant role in the protein adsorption capacity when the ionic strength of buffer solutions is very low. With the increase in ionic strength, the effect of the geometric structure on the protein adsorption capacity reduced greatly. The change of ionic strength has the highest significant effect on the mesoporous TiO₂ with large pore size compared with that with small pore size. The interaction between the protein and TiO₂ measured with atomic force microscopy further demonstrated that the adhesion force induced by the surface geometry reduced with the increase in the ionic strength. These findings were used to guide the detection of the retention behavior of protein by high-performance liquid chromatography, providing a step forward toward understanding the protein adsorption for predicting and controlling the chromatographic separation of proteins.

Science and art of protein formulation development

Protein pharmaceuticals have become a significant class of marketed drug products and are expected to grow steadily over the next decade. Development of a commercial protein product is, however, a rather complex process. A critical step in this process is formulation development, enabling the final product configuration. A number of challenges still exist in the formulation development process. This review is intended to discuss these challenges, to illustrate the basic formulation development processes, and to compare the options and strategies in practical formulation development.

Tetramer formation by the caspase-activated fragment of the Par-4 tumor suppressor

The prostate apoptosis response-4 (Par-4) tumor suppressor can selectively kill cancer cells via apoptosis while leaving healthy cells unharmed. Full length Par-4 has been shown to be predominantly intrinsically disordered in vitro under neutral conditions. As part of the apoptotic process, cellular Par-4 is cleaved at D131 by caspase-3, which generates a 24 kDa C-terminal activated fragment (cl-Par-4) that enters the nucleus and inhibits pro-survival genes, thereby preventing cancer cell proliferation. Here, the structure of cl-Par-4 was investigated using CD spectroscopy, dynamic light scattering, intrinsic tyrosine fluorescence, and size exclusion chromatography with mutli-angle light scattering. Biophysical characterization shows that cl-Par-4 aggregates and is disordered at low ionic strength. However, with increasing ionic strength, cl-Par-4 becomes progressively more helical and less aggregated, ultimately forming largely ordered tetramers at high NaCl concentration. These results, together with previous results showing induced folding at acidic pH, suggest that the in vivo structure and self-association state of cl-Par-4 may be strongly dependent upon cellular environment.

Do soft anions promote protein denaturation through binding interactions? A case study using ribonuclease A

It has long been known that large soft anions like bromide, iodide and thiocyanate are protein denaturing agents, but their mechanism of action is still unclear. In this work we have investigated the protein denaturing properties of these anions using Ribonuclease A (RNase A) as a model protein system. Salt-induced perturbations to the protein folding free energy were determined using differential scanning calorimetry and the results demonstrate that the addition of sodium iodide and sodium thiocyanate significantly decreases the melting temperature of the protein. In order to account for this reduction in protein stability, we show that the introduction of salts that contain soft anions to the aqueous solvent perturbs the protein unfolding free energy through three mechanisms: (a) screening Coulomb interactions that exist between charged protein residues, (b) Hofmeister effects, and (c) specific anion binding to CH and CH2 moieties in the protein polypeptide backbone. Using the micellization of 1,2-hexanediol as a ruler for hydrophobicity, we have devised a practical methodology that separates the Coulomb and Hofmeister contributions of salts to the protein unfolding free energy. This allowing us to isolate the contribution of soft anion binding interactions to the unfolding process. The analysis shows that binding contributions have the largest magnitude, confirming that it is the binding of soft anions to the polypeptide backbone that is the main promoter of protein unfolding.

Protection effect of polyols on Rhizopus chinensis lipase counteracting the deactivation from high pressure and high temperature treatment

The influence of polyols on Rhizopus chinensis lipase (RCL) was investigated under high pressure. The poor stability of RCL was observed at 500 MPa at 60 °C without polyols which protected RCL against the loss of activity. The lipase is more stable in phosphate buffer than in tris buffer despite the protection of polyols. The activity was maintained 63% by the sorbitol of 2 mol/L in Tris-HCl buffer but 73% in phosphate buffer after the treatment at 500 MPa and 60 °C for 25 min. The same protective effects could be observed at 1 mol/L of sorbitol, erythritol, xylitol, and mannitol. However, further increase of hydroxyl group number could not significantly improve the enzyme stability. The protection of polyols on RCL appears to depend on both of the polyol nature and the hydroxyl group number. Together with fluorescence spectra, circular dichroism spectra indicated that the chaotic conformation of RCL under high pressure became more ordered with 1 mol/L sorbitol. The results showed that sorbitol effectively stabilized the lipase conformation including the hydrophobic core under extreme conditions. It might be attributed to the interaction of polyols with RCL surface to modify intra-/intermolecular hydrogen bonds, maintaining the hydrophobic interactions within RCL.

Coupled effects of salt and pressure on catalytic ability of Rhizopus chinensis lipase

BACKGROUND

Both high pressure and environmental factors could influence the catalytic abilities of enzymes. This work investigated coupled effects of pressure and salts on Rhizopus chinensis lipase (RCL) to provide significant information for its further applications.

RESULTS

The maximum activity of RCL was observed under 200 MPa at 40 °C. The highest activity was achieved at concentrations of 0.06-0.1 mol L^-1 for tested salts. The effect of monovalent cations on RCL activity followed the Hofmeister series (K⁺ > Na⁺ > Li⁺ ) at 0.1 MPa but the order of Na⁺ and K⁺ was changed under 200 MPa. Meanwhile, the effects of anions did not follow the Hofmeister series. KCl slightly improved the thermostability of RCL at moderate concentration. At 60 °C, LiCl only stabilised RCL at 0.1 mol L^-1 . The pre-transition unfolding point was shifted from 4.5 to 3.5 mol L^-1 with pressure increasing from 0.1 to 600 MPa. In addition, KCl could not change the lipase's extrinsic fluorescence evolution versus pressure.

CONCLUSION

Pressure and salts could improve catalytic ability and stability of RCL under appropriate conditions. The effect of high pressure on RCL was influenced by salts. Meanwhile salts cannot prevent high pressure-induced damage to RCL. © 2017 Society of Chemical Industry.

Production of Isolated Giant Unilamellar Vesicles under High Salt Concentrations

The cell membrane forms a dynamic and complex barrier between the living cell and its environment. However, its in vivo studies are difficult because it consists of a high variety of lipids and proteins and is continuously reorganized by the cell. Therefore, membrane model systems with precisely controlled composition are used to investigate fundamental interactions of membrane components under well-defined conditions. Giant unilamellar vesicles (GUVs) offer a powerful model system for the cell membrane, but many previous studies have been performed in unphysiologically low ionic strength solutions which might lead to altered membrane properties, protein stability and lipid-protein interaction. In the present work, we give an overview of the existing methods for GUV production and present our efforts on forming single, free floating vesicles up to several tens of μm in diameter and at high yield in various buffer solutions with physiological ionic strength and pH.

Production of Isolated Giant Unilamellar Vesicles under High Salt Concentrations

The cell membrane forms a dynamic and complex barrier between the living cell and its environment. However, its in vivo studies are difficult because it consists of a high variety of lipids and proteins and is continuously reorganized by the cell. Therefore, membrane model systems with precisely controlled composition are used to investigate fundamental interactions of membrane components under well-defined conditions. Giant unilamellar vesicles (GUVs) offer a powerful model system for the cell membrane, but many previous studies have been performed in unphysiologically low ionic strength solutions which might lead to altered membrane properties, protein stability and lipid-protein interaction. In the present work, we give an overview of the existing methods for GUV production and present our efforts on forming single, free floating vesicles up to several tens of μm in diameter and at high yield in various buffer solutions with physiological ionic strength and pH.

Optimized conditions for preserving stability and integrity of porcine circovirus type2 virus-like particles during long-term storage

Although porcine circovirus type 2 (PCV2) virus-like particles (VLPs) have been successfully harvested from various protein expression systems, conditions to promote their stability and integrity during long-term storage have not been well defined since only the intact VLPs, instead of the monomeric capsid protein (Cap), can induce neutralizing antibodies in pigs in previous studies. In this study, freshly prepared PCV2 VLPs were stored in several media (various concentrations of NaCl, sorbitol, sucrose and trehalose) at three temperatures (4°C, -20°C and -80°C) and their stability and integration were evaluated after 7 month. Addition of 15% trehalose in storage buffer promoted long-term preservation of PCV2 VLPs. In contrast, storage buffer with 5% osmolytes (sucrose, trehalose and sorbitol) did not confer stabilization for long-term storage. These refined storage conditions for stabilization of PCV2 VLPs should enhance their use in vaccines.

One-step synthesis of glycoprotein mimics in vitro: improvement of protein activity, stability and application in CPP hydrolysis

Glycoprotein mimics produced in vitro by one-step conjugation of glycopolymer and pyrophosphatase have improved bioactivity and stability for potential biomedical applications.

Reconstruction of segmental bone defect of long bones after tumor resection by devitalized tumor-bearing bone

BACKGROUND

The reconstruction of an intercalary bone defect after a tumor resection of a long bone remains a challenge to orthopedic surgeons. Though several methods have been adopted to enhance the union of long segmental allografts or retrieved segmental autografts to the host bones, still more progresses are required to achieve a better union rate. Several methods have been adopted to devitalize tumor bone for recycling usage, and the results varied. We describe our experiences of using devitalized tumor-bearing bones for the repairing of segmental defects after tumor resection.

METHODS

Twenty-seven eligible patients treated from February 2004 to May 2012 were included. The segmental tumor bone (mean length, 14 cm) was resected, and then devitalized in 20% sterile saline at 65 °C for 30 min after the tumor tissue was removed. The devitalized bone was implanted back into the defect by using nails or plates.

RESULTS

Complete healing of 50 osteotomy ends was achieved at a median time of 11 months (interquartile range (IQR) 9-13 months). Major complications included bone nonunion in four bone junctions (7.4%), devitalized bone fracture in one patient (3.7%), deep infection in three patients (11.1%), and fixation failure in two patients (7.4%). The bone union rates at 1 and 2 years were 74.1 and 92.6%, respectively. The average functional score according to the Musculoskeletal Tumor Society (MSTS) 93 scoring system was 93 % (IQR 80-96.7%).

CONCLUSIONS

Incubation in 20% sterile saline at 65 °C for 30 min is an effective method of devitalization of tumor-bearing bone. The retrieved bone graft may provide as a less expensive alternative for limb salvage. The structural bone and the preserved osteoinductivity of protein may improve bone union.

Effects of ions on water structure: a low-field ¹H T₁ NMR relaxometry approach

Aqueous salt solutions play an important role in nature because of their effects on environmental biogeochemical processes and on structural properties of biomolecules. Upon dissolution, salts split in ions that are solvated. Water in hydration shells is subjected to molecular motions that can be monitored by (1)H T1 NMR relaxometry. This technique allowed the evaluation of the nature of the interactions between water and ions via variable temperature experiments. Examination of relaxometry properties of aqueous solutions at variable salt concentrations allowed acknowledgement of the role played by ions in either structuring or destructuring water aggregates. A mathematical model has been applied on six environmentally relevant salts: NaCl, KCl, CaCl2, CaCO3, NaNO3, and NH4NO3. It was linear only for the concentration dependence of KCl-R1. This model accorded with the one reported in literature where it has been considered valid only for diluted solutions. However, in the present study, the range of linearity for KCl was extended up to the saturation point. The model was modified for NaCl, CaCl2, and CaCO3 by using it as an exponential form in order to account for the nonlinearity of the R1-versus-concentration curves. Nonlinearity was explained by the nonnegligible ion-ion interactions occurring as concentration was increased. Finally, further modification was needed to account for the asymmetric distribution of water around nitrate (in NaNO3 and NH4NO3) and ammonium (in NH4NO3). This study is preliminary to the comprehension of the diffusion mechanisms of ions in water solutions at the equilibrium condition with solid surfaces such as soils and biochar-amended soils.

Sulfate anion delays the self-assembly of human insulin by modifying the aggregation pathway

The understanding of the molecular mechanisms underlying protein self-assembly and of their dependence on solvent composition has implications in a large number of biological and biotechnological systems. In this work, we characterize the aggregation process of human insulin at acidic pH in the presence of sulfate ions using a combination of Thioflavin T fluorescence, dynamic light scattering, size exclusion chromatography, Fourier transform infrared spectroscopy, and transmission electron microscopy. It is found that the increase of sulfate concentration inhibits the conversion of insulin molecules into aggregates by modifying the aggregation pathway. At low sulfate concentrations (0-5 mM) insulin forms amyloid fibrils following the nucleated polymerization mechanism commonly observed under acidic conditions in the presence of monovalent anions. When the sulfate concentration is increased above 5 mM, the sulfate anion induces the salting-out of ∼18-20% of insulin molecules into reversible amorphous aggregates, which retain a large content of α-helix structures. During time these aggregates undergo structure rearrangements into β-sheet structures, which are able to recruit monomers and bind to the Thioflavin T dye. The alternative aggregation mechanism observed at large sulfate concentrations is characterized by a larger activation energy and leads to more polymorphic structures with respect to the self-assembly in the presence of chloride ions. The system shown in this work represents a case where amorphous aggregates on pathway to the formation of structures with amyloid features could be detected and analyzed.

Specific recognition of guanines in non-duplex regions of nucleic acids with potassium tungstate and hydrogen peroxide

Structural features of nucleic acids have become an integral part of current biomedical research. Highly selective and readily performed methods with little toxicity that target guanosines in non-duplex nucleic acids are needed, which led us to search for an effective agent for guanosine sequencing. Treatment of DNA or RNA with potassium tungstate and hydrogen peroxide produced damaged guanosines in DNA or RNA sequences. The damaged guanosines in non-duplex DNA could be cleaved by hot piperidine. Similarly, damaged guanosines in non-duplex RNA could be cleaved by aniline acetate. We could identify structural features of nucleic acid using this strategy instead of dimethyl sulphate and Ribonuclease T1.

Tetramers are the activation-competent species of the HOCl-specific transcription factor HypT

Hypochlorous acid (HOCl) is an important component of the immune system and is produced by neutrophils to kill invading microorganisms. The transcription factor HypT is specifically activated by HOCl by methionine oxidation and protects Escherichia coli cells from the detrimental effects of HOCl. HypT forms dodecameric ring-like oligomers. Binding of HypT to DNA induces dissociation of the dodecamers into dimers and tetramers, thus forming the DNA-binding species. To dissect HypT dissociation, binding to DNA, and activation, we aimed to dissociate the dodecamers independently of DNA and to analyze HOCl-dependent activation in vitro. We found that HypT dodecamers dissociated into tetramers in the presence of l-arginine and NaCl, which was reversible upon dilution of the additive. Making use of the reversible dissociation, we generated mixed assemblies consisting of wild-type and mutant HypT subunits and determined that mutant subunits with reduced thermal stability were stabilized by wild-type HypT in the mixed assembly. HypT tetramers, as present at high NaCl concentrations, were stabilized against thermal unfolding and aggregation triggered by high HOCl concentrations. Importantly, in vitro activation by HOCl of HypT tetramers was completed within 1 min, whereas activation of dodecamers required 1 h for completion. Furthermore, activation of HypT tetramers required stoichiometric amounts of HOCl instead of an excess of HOCl, as observed for dodecamers. This supports the idea that small HypT oligomers are the activation-competent species, whereas the dodecamers are a storage form. Our study reveals the importance of the dynamic oligomeric state for HypT activation by HOCl.