Equilibrium study of protein denaturation by urea

Spherulite formation in green nonaqueous media: The impact of urea on gelation in glycerol

HYPOTHESIS

Large macroscopic assemblies formed by a surfactant, sodium dodecylsulfate (SDS), and glycerol, can be directed to assemble in a hierarchical manner by the addition of a strong hydrogen-bond donor/acceptor, such as urea.

CONTEXT

Self-assembly in complex media is important to a range of applications, for instance in biological media, which are multi-component, to industrial formulations, where additives are present for flavour, texture, and preservation. Here, the gelation and self-assembly of sodium dodecylsulfate (SDS) in glycerol is explored in the presence of an additive, urea. Urea was chosen due to its importance both fundamentally and industrially, but also because of its ability to form strong H-bonds and interact with both glycerol and SDS.

EXPERIMENTAL

To cover the variety of length scales present in the gel-like phase, a combination of optical microscopy and small-angle X-ray scattering techniques were used to probe the micro- to nanoscale.

FINDINGS

On the microscale, the formation of a spectacular spherulite phase, even at low urea contents - 0.1 wt%, upon cooling was observed, a stark difference to the microfibrillar phase observed in the absence of urea. Interestingly, the nanostructure of the two crystalline phases were similar and showed negligible differences. This suggests that urea is not involved in the SDS/glycerol microfibril formation but instead directs the assembly of spherulites by bundling the microfibrils. These ternary systems are also probed as a function of urea content, SDS concentration, and temperature. The observations in this work highlight the importance of small molecules in the self-assembly process, which is relevant both fundamentally but also industrially, where small molecules are often added to formulations.

Electron Capture vs Transfer Dissociation for Site Determination of Tryptic Peptide Tyrosine Sulfation: Direct Detection of Fibrinogen Sulfation Sites and Identification of Novel Isobaric Interferences

Tyrosine sulfation, an understudied but crucial post-translational modification, cannot be directly detected in conventional nanoflow liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) due to the extreme sulfate lability. Here, we report the detection of sulfate-retaining fragments from LC-electron capture dissociation (ECD) and nanoLC-electron transfer higher energy collision dissociation (EThcD). Sulfopeptide candidates were identified by Proteome Discoverer and MSFragger analysis of nanoLC-HCD MS/MS data and added to inclusion lists for LC-ECD or nanoLC-EThcD MS/MS. When this approach failed, targeted LC-ECD with fixed m/z isolation windows was performed. For the plasma protein fibrinogen, the known pyroglutamylated sulfopeptide QFPTDYDEGQDDRPK from the beta chain N-terminus was identified despite a complete lack of sulfate-containing fragment ions. The peptide QVGVEHHVEIEYD from the gamma-B chain C-terminus was also identified as sulfated or phosphorylated. This sulfopeptide is not annotated in Uniprot but was previously reported. MSFragger further identified a cysteine-containing peptide from the middle of the gamma chain as sulfated and deamidated. NanoLC-EThcD and LC-ECD MS/MS confirmed the two former sulfopeptides via sulfate-retaining fragment ions, whereas an unexpected fragmentation pattern was observed for the third sulfopeptide candidate. Manual interpretation of the LC-ECD spectrum revealed two additional isobaric identifications: a trisulfide-linked cysteinyl-glycine or a carbamidomethyl-dithiothreiotol covalent adduct. Synthesis of such adducts confirmed the latter identity.

Cholesterol and Lipid Rafts in the Biogenesis of Amyloid-β Protein and Alzheimer's Disease

Cholesterol has been conjectured to be a modulator of the amyloid cascade, the mechanism that produces the amyloid-β (Aβ) peptides implicated in the onset of Alzheimer's disease. We propose that cholesterol impacts the genesis of Aβ not through direct interaction with proteins in the bilayer, but indirectly by inducing the liquid-ordered phase and accompanying liquid-liquid phase separations, which partition proteins in the amyloid cascade to different lipid domains and ultimately to different endocytotic pathways. We explore the full process of Aβ genesis in the context of liquid-ordered phases induced by cholesterol, including protein partitioning into lipid domains, mechanisms of endocytosis experienced by lipid domains and secretases, and pH-controlled activation of amyloid precursor protein secretases in specific endocytotic environments. Outstanding questions on the essential role of cholesterol in the amyloid cascade are identified for future studies.

Protecting Proteins from Desiccation Stress Using Molecular Glasses and Gels

Faced with desiccation stress, many organisms deploy strategies to maintain the integrity of their cellular components. Amorphous glassy media composed of small molecular solutes or protein gels present general strategies for protecting against drying. We review these strategies and the proposed molecular mechanisms to explain protein protection in a vitreous matrix under conditions of low hydration. We also describe efforts to exploit similar strategies in technological applications for protecting proteins in dry or highly desiccated states. Finally, we outline open questions and possibilities for future explorations.

Interactions of adsorbing cosolutes with hydrophobic hydration shells

The analysis of water density fluctuations in the hydration shell of nonpolar solutes provides insights into water-mediated interactions, especially hydrophobic interactions. These fluctuations are sensitive to small perturbations due to changes in thermodynamic conditions, such as temperature and pressure, but also to the presence of cosolutes, such as salts or small organic molecules. Herein, we investigate the effect of two classes of adsorbing cosolutes, using urea and methanol as representatives, on the fluctuations in energy and solvent density within the solvation shell of a model extended hydrophobic solute. We focus on the interactions of the cosolutes with the hydrophobic hydration shell, rather than with the solute itself, which though important remain largely unexplored. We calculate and analyze the interfacial partial molar energy of the cosolute, using a methodology based on the small system method. This approach provides correlated solvent density and energy fluctuations and allows us to decompose them into contributions due to interactions between the different components present in the solvation shell of the solute. The results show that adsorbed urea molecules interact more favorably with water than nonadsorbed urea molecules, which leads to the attenuation of interfacial density fluctuations and thus to the stabilization of the solvation shell. By contrast, the adsorbed methanol molecules interact preferably with other methanol molecules in the solvation shell, leading to a nano-phase segregated structure, which enhances interfacial fluctuations.

Trimethylamine-N-oxide depletes urea in a peptide solvation shell

Trimethylamine-N-oxide (TMAO) and urea are metabolites that are used by some marine animals to maintain their cell volume in a saline environment. Urea is a well-known denaturant, and TMAO is a protective osmolyte that counteracts urea-induced protein denaturation. TMAO also has a general protein-protective effect, for example, it counters pressure-induced protein denaturation in deep-sea fish. These opposing effects on protein stability have been linked to the spatial relationship of TMAO, urea, and protein molecules. It is generally accepted that urea-induced denaturation proceeds through the accumulation of urea at the protein surface and their subsequent interaction. In contrast, it has been suggested that TMAO's protein-stabilizing effects stem from its exclusion from the protein surface, and its ability to deplete urea from protein surfaces; however, these spatial relationships are uncertain. We used neutron diffraction, coupled with structural refinement modeling, to study the spatial associations of TMAO and urea with the tripeptide derivative glycine-proline-glycinamide in aqueous urea, aqueous TMAO, and aqueous urea-TMAO (in the mole ratio 1:2 TMAO:urea). We found that TMAO depleted urea from the peptide's surface and that while TMAO was not excluded from the tripeptide's surface, strong atomic interactions between the peptide and TMAO were limited to hydrogen bond donating peptide groups. We found that the repartition of urea, by TMAO, was associated with preferential TMAO-urea bonding and enhanced urea-water hydrogen bonding, thereby anchoring urea in the bulk solution and depleting urea from the peptide surface.

The application of nanoparticles-based ferroptosis, pyroptosis and autophagy in cancer immunotherapy

Immune checkpoint blockers (ICBs) have been applied for cancer therapy and achieved great success in the field of cancer immunotherapy. Nevertheless, the broad application of ICBs is limited by the low response rate. To address this issue, increasing studies have found that the induction of immunogenic cell death (ICD) in tumor cells is becoming an emerging therapeutic strategy in cancer treatment, not only straightly killing tumor cells but also enhancing dying cells immunogenicity and activating antitumor immunity. ICD is a generic term representing different cell death modes containing ferroptosis, pyroptosis, autophagy and apoptosis. Traditional chemotherapeutic agents usually inhibit tumor growth based on the apoptotic ICD, but most tumor cells are resistant to the apoptosis. Thus, the induction of non-apoptotic ICD is considered to be a more efficient approach for cancer therapy. In addition, due to the ineffective localization of ICD inducers, various types of nanomaterials have been being developed to achieve targeted delivery of therapeutic agents and improved immunotherapeutic efficiency. In this review, we briefly outline molecular mechanisms of ferroptosis, pyroptosis and autophagy, as well as their reciprocal interactions with antitumor immunity, and then summarize the current progress of ICD-induced nanoparticles based on different strategies and illustrate their applications in the cancer therapy.

Performance and mechanisms of urea exposure for enhancement of biotransformation of sewage sludge into volatile fatty acids

Herein, a cost-effective method for improving the anaerobic fermentation performance of sewage sludge (SS) is proposed. The highest volatile fatty acids (VFAs) reached up to 5550 mg COD/L with the supplementation of 0.2 g urea/g total suspended solids (TSS). Intensive exploration showed that SS decomposition was profoundly triggered by urea and the free ammonia generated due to the hydrolysis of urea, providing adequately bioaccessible substrates for acidogenic reactions and thus contributing to VFAs formation. Microbial composition analysis indicated that functional bacteria (i.e., Tissierella and Clostridium) associated with VFAs generation were enriched. Moreover, the metabolic activities of functional flora (i.e., membrane transport and fatty acid synthesis) were up-regulated due to the stimulation of urea. In general, the increase in bioavailable organic matter and functional microbes, and thus the increased microbial metabolic activities, improved the efficient production of VFAs. This study could provide a cost-effective approach for resource recovery from SS.

Not Always Sticky: Specificity of Protein Stabilization by Sugars Is Conferred by Protein-Water Hydrogen Bonds

Solutes added to buffered solutions directly impact protein folding. Protein stabilization by cosolutes or crowders has been shown to be largely driven by protein-cosolute volume exclusion complemented by chemical and soft interactions. By contrast to previous studies that indicate the invariably destabilizing role of soft protein-sugar attractions, we show here that soft interactions with sugar cosolutes are protein-specific and can be stabilizing or destabilizing. We experimentally follow the folding of two model miniproteins that are only marginally stable but in the presence of sugars and polyols fold into representative and distinct secondary structures: β-hairpin or α-helix. Our mean-field model reveals that while protein-sugar excluded volume interactions have a similar stabilizing effect on both proteins, the soft interactions add a destabilizing contribution to one miniprotein but further stabilize the other. Using molecular dynamics simulations, we link the soft protein-cosolute interactions to the weakening of direct protein-water hydrogen bonding due to the presence of sugars. Although these weakened hydrogen bonds destabilize both the native and denatured states of the two proteins, the resulting contribution to the folding free energy can be positive or negative depending on the amino acid sequence. This study indicates that the significant variation between proteins in their soft interactions with sugar determines the specific response of different proteins, even to the same sugar.

In Situ Observation of Chemically Induced Protein Denaturation at Solvated Interfaces

Proteins unfold in chaotropic salt solutions, a process that is difficult to observe at the single protein level. The work presented here demonstrates that a liquid-based atomic force microscope and graphene liquid-cell-based scanning transmission electron microscope make it possible to observe chemically induced protein unfolding. To illustrate this capability, ferritin proteins were deposited on a graphene surface, and the concentration-dependent urea- or guanidinium-induced changes of morphology were monitored for holo-ferritin with its ferrihydrite core as well as apo-ferritin without this core. Depending on the chaotropic agent the liquid-based imaging setup captured an unexpected transformation of natively folded holo-ferritin proteins into rings after urea treatment but not after guanidinium treatment. Urea treatment of apo-ferritin did not result in nanorings, confirming that nanorings are a specific signature of denaturation of holo-ferritins after exposture to sufficiently high urea concentrations. Mapping the in situ images with molecular dynamics simulations of ferritin subunits in urea solutions suggests that electrostatic destabilization triggers denaturation of ferritin as urea makes direct contact with the protein and also disrupts the water H-bonding network in the ferritin solvation shell. Our findings deepen the understanding of protein denaturation studied using label-free techniques operating at the solid-liquid interface.

Molecular mechanism of the common and opposing cosolvent effects of fluorinated alcohol and urea on a coiled coil protein

Alcohols and urea are widely used as effective protein denaturants. Among monohydric alcohols, 2,2,2-trifluoroethanol (TFE) has large cosolvent effects as a helix stabilizer in proteins. In contrast, urea efficiently denatures ordered native structures, including helices, into coils. These opposing cosolvent effects of TFE and urea are well known, even though both preferentially bind to proteins; however, the underlying molecular mechanism remains controversial. Cosolvent-dependent relative stability between native and denatured states is rigorously related to the difference in preferential binding parameters (PBPs) between these states. In this study, GCN4-p1 with two-stranded coiled coil helices was employed as a model protein, and molecular dynamics simulations for the helix dimer and isolated coil were conducted in aqueous solutions with 2 M TFE and urea. As 2 M cosolvent aqueous solutions did not exhibit clustering of cosolvent molecules, we were able to directly investigate the molecular origin of the excess PBP without considering the enhancement effect of PBPs arising from the concentration fluctuations. The calculated excess PBPs of TFE for the helices and those of urea for the coils were consistent with experimentally observed stabilization of helix by TFE and that of coil by urea. The former was caused by electrostatic interactions between TFE and side chains of the helices, while the latter was attributed to both electrostatic and dispersion interactions between urea and the main chains. Unexpectedly, reverse-micelle-like orientations of TFE molecules strengthened the electrostatic interactions between TFE and the side chains, resulting in strengthening of TFE solvation.

Counteracting Effects of Trimethylamine N-Oxide against Urea in Aqueous Solutions: Insights from Theoretical Two-Dimensional Infrared Spectroscopy

The study of small osmolytes in their aqueous solutions has gained significant attention because of their relevance to structure and thermodynamics of proteins in aqueous media. Special attention has been given to the binary and ternary aqueous solutions of urea and trimethylamine N-oxide (TMAO). Urea is a well-known protein denaturant, while TMAO protects proteins in their native states. Interestingly, TMAO counteracts urea's ability to denature proteins when present in solutions with approximately half of the concentration of urea. Vibrational spectroscopy can improve our understanding of the molecular origin of this counteracting effect because of its sensitivity to local structure and dynamics. We present results of theoretical linear vibrational and two-dimensional infrared (2DIR) spectroscopy of water in the binary and ternary aqueous solutions of TMAO and urea. The 2DIR spectra are calculated using the electronic structure/molecular dynamics approach. The non-Condon effects in spectral transitions are incorporated in the theoretical calculations of 2DIR spectra. It is found that TMAO disrupts the local structure of water, while urea leaves it essentially unaffected. The 2DIR results show that both TMAO and urea slow down the dynamics of spectral diffusion of water. The extent of slowing down is found to be particularly significant for both hydration and bulk water in the presence of TMAO which can be attributed to strong hydrogen bonds between the water and TMAO molecules. The water molecules present in the hydration layer of the solutes in the ternary solutions are found to relax at even slower rates compared to that in their binary solutions in water. The hydrogen bonds between TMAO and urea are found to be not stable. Thus, the counteracting effect of TMAO against urea is seen to take place mainly through water-mediated interactions. Such TMAO-induced effects giving rise to more structured and slower hydrogen-bonded network are successfully captured through 2DIR spectroscopic calculations.

Characterization of a fungal α-galactosidase and its synergistic effect with β-mannanase for hydrolysis of galactomannan

An acid stable α-galactosidase was produced and purified from mannolytic fungal strain, Penicillium aculeatum APS1. Enzyme was produced using wheat bran and copra cake moistened with corn steep liquor by solid state fermentation. APS1αgal having molecular weight of 65.4 kDa was purified to electrophoretic homogeneity by three phase partitioning and gel permeation chromatography with high enzyme recovery. APS1αgal was found to be maximally active at 55 °C and pH 4.5, having high stability at acidic pH. Thermal stability and thermal inactivation kinetics of APS1αgal were also studied. APS1αgal was found to effectively hydrolyse oligosaccharides as well as polysaccharides having α-1,6 linked galactose. Abolishment of enzyme activity in N-brommosuccinimide revealed an important role of tryptophan residue in catalysis. APS1αgal had shown outstanding tolerance to NaCl and proteases. MALDI-TOF MS/MS analysis indicated that enzyme is probably a member of family GH27. Synergistic interaction between APS1αgal and β-mannanase for hydrolysis of galactomannan was very clear and maximum 2.0° of synergy was found under simultaneous mode of action. This study reports a new source of α-galactosidase with biochemical properties suitable for applications in food and feed industries.

Osmolytes: Wonder molecules to combat protein misfolding against stress conditions

The proper functioning of any protein depends on its three dimensional conformation which is achieved by the accurate folding mechanism. Keeping away from the exposed stress conditions leads to cooperative unfolding and sometimes partial folding, forming the structures like protofibrils, fibrils, aggregates, oligomers, etc. leading to several neurodegenerative diseases like Parkinson's disease, Alzheimer's, Cystic fibrosis, Huntington, Marfan syndrome, and also cancers in some cases, too. Hydration of proteins is necessary, which may be achieved by the presence of organic solutes called osmolytes within the cell. Osmolytes belong to different classes in different organisms and play their role by preferential exclusion of osmolytes and preferential hydration of water molecules and achieves the osmotic balance in the cell otherwise it may cause problems like cellular infection, cell shrinkage leading to apoptosis and cell swelling which is also the major injury to the cell. Osmolyte interacts with protein, nucleic acids, intrinsically disordered proteins by non-covalent forces. Stabilizing osmolytes increases the Gibbs free energy of the unfolded protein and decreases that of folded protein and vice versa with denaturants (urea and guanidinium hydrochloride). The efficacy of each osmolyte with the protein is determined by the calculation of m value which reflects its efficiency with protein. Hence osmolytes can be therapeutically considered and used in drugs.

Nanopore single-molecule biosensor in protein denaturation analysis

Unclear issues in protein studies include but not limited to the stability and denaturation mechanism in the presence of denaturants. Herein, we report a dynamic monitoring approach based on nanopore single-molecule biosensor, which can detect the protein's folding and unfolding transitions by recording a nanopore ionic current. When gradually increasing the concentration of denaturant guanidine hydrochloride (GdmCl), sensitive responses were observed with lysozyme unfolding. The emergence of the featured biphasic-pulse demonstrated the existence of a stable intermediate. It was the first time to experimentally confirm the dynamic equilibrium between the intermediate and the native states at single molecule level, therefore consolidating the standpoint of lysozyme denaturation process following the three-state model. Additionally, we got more insights into the conformation about the intermediate as globular-like structure, larger gyration radius, and enhanced positive charge density. We considered that the manner of denaturant toward lysozyme adopts the "direct" model based on stronger electrostatic and van der Waals forces. Nanopore biosensor exhibited excellent sensitivity with a low detection concentration of 280 pM and reproducibility in analysing the folding intermediate of lysozyme.

Colorimetric Sensor Array for Identification of Proteins and Classification of Metabolic Profiles under Various Osmolyte Conditions

Rapid and efficient detection and identification of proteins hold great promise in medical diagnostics, treatment of different diseases, and proteomics. Here, we present a simple colorimetric sensor array for the differentiation of proteins in various osmolyte solutions. Osmolytes have different influences on the conformation of proteins, which have differential binding to silver nanoparticles, resulting in color changes. The sensor array shows unique color change patterns for each of the 19 proteins, allowing unambiguous identification. Very interestingly, the differentiation of 19 proteins is related to their molecular weight. Moreover, the sensor array can be used to identify protein mixtures, thermal denaturized proteins, and unknown protein samples. Finally, the sensor array can also analyze the plasma or liver samples of the four groups of salt-sensitive rats fed with different diets, indicating that it has the potential for the classification of metabolic profiles.

Conformational Features and Hydration Dynamics of Proteins in Cosolvents: A Perspective from Computational Approaches

The importance of solvent in stabilizing protein structures has long been recognized. Water is the common solvent for proteins, and hydration is elemental in governing protein stability, flexibility, and function through various interactions. The addition of small organic molecules known as cosolvents may deploy stabilization (folding) or destabilization (unfolding) effects on native protein conformations. Despite exhaustive literature, the molecular mechanism by which cosolvents regulate protein conformations and dynamics is controversial. Specifically, the cosolvent behavior has been unpredictable with the nature and concentrations that lead to protein stabilizing/destabilizing effects as it changes in water content near the vicinity of proteins. With the massive development of computational resources, advancement of computational methods, and the availability of numerous experimental techniques, various theoretical and computational studies of proteins in a mixture of solvents have been instigated. The growing interest in such studies has been to unravel the underlying mechanism of protein folding and cosolvent/solvent-protein interactions that have significant implications in biomedical and biotechnological applications. In this mini-review, apart from the brief overview of important theories and force-field model-based cosolvent effects on proteins, we present the current state of knowledge and recent advances in the field to describe cosolvent-guided conformational features of proteins and hydration dynamics from computational approaches. The mini-review further explains the mechanistic details of protein stability in various popularly used cosolvents, including limitations of present studies and future outlooks. The counteracting effects of cosolvent on the proteins in the mixture of stabilizing and destabilizing cosolvents are also presented and discussed.

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.

Unveiling the Mechanism of Urine Source Separation-Derived Pretreatment on Enhancing Short-Chain Fatty Acid Yields from Anaerobic Fermentation of Waste Activated Sludge

A novel strategy employing urine wastewater derived from source separation technology, to pretreat waste activated sludge (WAS) for promoting yields of short-chain fatty acids (SCFAs), has been proposed in this study. It was found experimentally that SCFA production could ascend up to 305.4 mg COD/g VSS (volatile suspended solids) with a urine volumetric proportion of 1:2 to the whole reaction system, being 8.8 times that produced in the control. Exploration of the mechanism indicated that WAS disintegration was significantly enhanced due to the synergistic effect of urea and free ammonia (FA). Degradation rates of model organic substrates and measurements of critical enzymatic activities demonstrated that hydrolysis and acidogenesis were inhibited under high urine content (urine proportion of 1:2), while not significantly affected under low urine content (i.e., 1:4), which might be attributed to metal ions existing in urine wastes alleviating the inhibition induced by FA. In contrast, methanogenesis was negatively suppressed by any urine concentration owing to its higher sensitivity to the environmental variations. Shift of microbial population further elucidated the abundance of hydrolytic and acidogenic microbes were enriched in the fermenters with urine addition. The findings provide a new thought for recovering resources from wastes, potentially reducing the pressure of sewage and sludge treatment in wastewater treatment plants.

Significantly improved detection performances of immunoassay for ractopamine in urine based on highly urea-tolerant rabbit monoclonal antibody

Highly sensitive and accurate screening of ractopamine (RAC) residue in animal urine is greatly needed to ensure food security. The detection performance of immunoassay for RAC was always seriously harmed by the antibody inactivation derived from urea. Here, we first discovered one rabbit monoclonal antibody (RmAb) to RAC with a high affinity of 0.007 ng mL^-1 and a surprising urea tolerance of 3 M urea, which is beneficial for developing robustly developed immunoassay in urine without sample pretreatment. The limits of detection of developed indirect competitive enzyme-linked immunosorbent assay based on RmAb1 for RAC were 0.0042-0.014 μg L^-1 with the coefficient of variation below 11.7% in swine, sheep, and cow urine, significantly improved 10-100-fold in sensitivity. Moreover, the urea-tolerant mechanism of RmAb1 showed that more non-polar amino acids, more hydrogen bond donors on the surface, and preponderant Pi interaction of antibody-RAC all contributed to the stability of the RmAb1 in a high concentration of urea.

A Transfer Free Energy Based Implicit Solvent Model for Protein Simulations in Solvent Mixtures: Urea-Induced Denaturation as a Case Study

We developed a method for implicit solvent molecular dynamics simulations of proteins in solvent mixtures (model with implicit solvation thermodynamics, MIST). The MIST method introduces experimental group transfer free energies to the generalized Born formulation for generating molecular trajectories without the need for developing rigorous explicit-solvent force fields for multicomponent solutions. As a test case, we studied the urea-induced denaturation of the Trp-cage miniprotein in water. We demonstrate that our method allows efficient exploration of the conformational space of the protein in only a few hundreds of nanoseconds of all-atom unbiased simulations. Furthermore, selective implementation of the transfer free energies of specific peptide groups, backbone, and side chains enables us to decouple their specific energetic contributions to the conformational changes of the protein. The approach herein developed can readily be extended to the investigation of complex matrices as well as to the characterization of protein aggregation. The MIST method is implemented in Plumed (ver. 2.8) as a separate module called SASA.

In silico studies of the human IAPP in the presence of osmolytes

The human islet amyloid polypeptide or amylin is secreted along with insulin by pancreatic islets. Under the drastic environmental conditions, amylin can aggregate to form amyloid fibrils. This amyloid plaque of hIAPP in the pancreatic cells is the cause of type II diabetes. Early stages of amylin aggregates are more cytotoxic than the matured fibrils. Here, we have used the all-atom molecular dynamic simulation to see the effect of water, TMAO, urea and urea/TMAO having ratio 2:1 of different concentrations on the amylin protein. Our study suggest that the amylin protein forms β-sheets in its monomeric form and may cause the aggregation of protein through the residue 13-17 and the C-terminal region. α-Helical content of protein increases with an increase in TMAO concentration by decreasing the SASA value of protein, increase in intramolecular hydrogen bonds and on making the short-range hydrophobic interactions. Electrostatic potential surfaces show that hydrophobic groups are buried and normalised configurational entropy of backbone, and side-chain atoms is lesser in the presence of TMAO, whereas opposite behaviour is obtained in the case of urea. Counteraction effect of TMAO using Kast model towards urea is also observed in ternary solution of urea/TMAO.

Monitoring Protein Global and Local Parameters in Unfolding and Binding Studies: The Extended Applicability of the Diffusion Coefficient─Molecular Size Empirical Relations

Protein unfolding and denaturation are main issues in biochemical and pharmaceutical research. Using a global parameter, the translational diffusion coefficient D, folded, unfolded, and intrinsically disordered proteins of a given molar mass M can be distinguished based on their distinct hydrodynamic properties. For broader applications, we provide generalized, PFG-NMR-based empirical D-M relations validated at different temperatures and ready to use with the corresponding corrections in different media. We demonstrate that these relations enable a more accurate molecular mass determination and show fewer potential errors than those of the common methods based on small-molecular diffusion standards. We monitor unfolding of three model proteins using 8 M urea and dimethyl sulfoxide (DMSO)-water mixtures as denaturing agents, highlighting the effect of disulfide bonds. Denaturation in 8 M urea is pH-dependent; in addition, for proteins with highly stable disulfide bonds, a reducing agent (TCEP) is required to achieve complete unfolding. Regarding the effect of local parameters, we show that at low DMSO concentrations─common conditions in pharmaceutical binding studies─the PFG-NMR-derived global parameters are not significantly affected. Still, the atomic environments can change, and the bound solvent molecule can inhibit the binding of a partner molecule. Using proteins with natural isotopic abundance, this effect can be proven by fast ¹H-¹⁵N 2D correlation spectra. Our results enable fast and easy estimation of protein molecular mass and the degree of folding in various media; moreover, the effect of the cosolvent on the atomic-level structure can be traced without the need of isotope labeling.

Solvation shell thermodynamics of extended hydrophobic solutes in mixed solvents

The ability of various cosolutes and cosolvents to enhance or quench solvent density fluctuations at solute–water interfaces has crucial implications on the conformational equilibrium of macromolecules such as polymers and proteins. Herein, we use an extended hydrophobic solute as a model system to study the effect of urea and methanol on the density fluctuations in the solute’s solvation shell and the resulting thermodynamics. On strengthening the solute–water/cosolute repulsive interaction, we observe distinct trends in the mutual affinities between various species in, and the thermodynamic properties of, the solvation shell. These trends strongly follow the respective trends in the preferential adsorption of urea and methanol: solute–water/cosolute repulsion strengthens, urea accumulation decreases, and methanol accumulation increases. Preferential accumulation of urea is found to quench the density fluctuations around the extended solute, leading to a decrease in the compressibility of the solvation shell. In contrast, methanol accumulation enhances the density fluctuations, leading to an increase in the compressibility. The mode of action of urea and methanol seems to be strongly coupled to their hydration behavior. The observations from this simple model is discussed in relation to urea driven swelling and methanol induced collapse of some well-known thermo-responsive polymers.

Hydrophobic association and solvation of neopentane in urea, TMAO and urea-TMAO solutions

A detailed knowledge of hydrophobic association and solvation is crucial for understanding the con-formational stability of proteins and polymers in osmolyte solutions. Using molecular dynamics simulations, it is found that the hydrophobic association of neopentane molecules is greater in a mixed urea-TMAO-water solution in comparison to that in 8 M urea solution, 4 M TMAO solution and neat water. The neopentane association in urea solution is greater than that in TMAO solution or neat water. We find the association is even less in TMAO solution than pure water. From free energy calculations, it is revealed that the neopentane sized cavity creation in mixed urea-TMAO-water is most unfavorable and that causes the highest hydrophobic association. The cavity formation in urea solution is either more unfavorable or comparable to that in TMAO solution. Importantly, it is found that the population of neopentane-neopentane contact pair and the free energy contribution for the cavity formation step in TMAO solution are very sensitive towards the choice of TMAO force-fields. A careful construction of TMAO force-fields is important for studying the hydrophobic association. Interestingly it is observed that the total solute-solvent dispersion interaction energy contribution is always the most favorable in mixed urea-TMAO-water. The magnitude of this interaction energy is greater in urea solution relative to TMAO solution for two different force-fields of TMAO, whereas the lowest value is obtained in pure water. It is revealed that the extent of the overall hydrophobic association in osmolyte solutions is mainly governed by the cavity creation step and it nullifies the contribution coming from the solute-solvent interaction contribution.

Viscoelastic analysis of mussel threads reveals energy dissipative mechanisms

Mussels use byssal threads to secure themselves to rocks and as shock absorbers during cyclic loading from wave motion. Byssal threads combine high strength and toughness with extensibility of nearly 200%. Researchers attribute tensile properties of byssal threads to their elaborate multi-domain collagenous protein cores. Because the elastic properties have been previously scrutinized, we instead examined byssal thread viscoelastic behaviour, which is essential for withstanding cyclic loading. By targeting protein domains in the collagenous core via chemical treatments, stress relaxation experiments provided insights on domain contributions and were coupled with in situ small-angle X-ray scattering to investigate relaxation-specific molecular reorganizations. Results show that when silk-like domains in the core were disrupted, the stress relaxation of the threads decreased by nearly 50% and lateral molecular spacing also decreased, suggesting that these domains are essential for energy dissipation and assume a compressed molecular rearrangement when disrupted. A generalized Maxwell model was developed to describe the stress relaxation response. The model predicts that maximal damping (energy dissipation) occurs at around 0.1 Hz which closely resembles the wave frequency along the California coast and implies that these materials may be well adapted to the cyclic loading of the ambient conditions.

Gold nanodoughnut as an outstanding nanoheater for photothermal applications

Photoinduced hyperthermia is a cancer therapy technique that induces death to cancerous cells via heat generated by plasmonic nanoparticles. While previous studies have shown that some nanoparticles can be effective at killing cancer cells under certain conditions, there is still a necessity (or the need) to improve its heating efficiency. In this work, we perform a detailed theoretical study comparing the thermoplasmonic response of the most effective nanoparticle geometries up to now with a doughnut-shaped nanoparticle. We numerically demonstrate that the latter exhibits a superior tunable photothermal response in practical illumination conditions (unpolarized light). Furthermore, we show that nanoparticle heating in fluidic environments, i.e., nanoparticles undergoing Brownian rotations, strongly depends on the particle orientation with respect to the illumination source. We conclude that nanodoughnuts are the best nanoheaters in our set of structures, with an average temperature increment 40% higher than the second best nanoheater (nanodisk). Furthermore, nanodoughnuts feature a weak dependence on orientation, being therefore ideal candidates for photothermal therapy applications. Finally, we present a designing guide, covering a wide range of toroid designs, which can help on its experimental implementation.

Effects of water on the solvation and structure of lipase in deep eutectic solvents containing a protein destabilizer and stabilizer

Aqueous deep eutectic solvent (DES) solutions emerge as new media for biocatalysis. The large number of DESs provides a space for designing solutions with desired features. One challenge for this design is to understand the fundamental relationship between the water effect on biocatalysis and the DES compositions. We investigate the solvation and structure of a lipase protein in two DESs containing a protein destabilizer (choline : urea (1 : 2)) and stabilizer (choline : glycerol (1 : 2)) and their 1 : 1 aqueous solution using molecular dynamics simulations. The lipase protein in the pure aqueous solution is simulated as the reference. The lipase protein remains folded in both DESs and their aqueous solutions. In both DESs, water molecules weaken the solvation shell of the lipase protein by reducing the protein-DES hydrogen bond lifetimes. However, the water molecules change the surface area and conformation of the active site on the lipase protein differently in the two DESs. Our simulations indicate that the impact on active sites plays an important role in differentiating the effect of water on biocatalysis in aqueous DESs.

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.

Purification and erythrocyte-membrane perturbing activity of a ketose-specific lectin from Moringa oleifera seeds

This study purified a hemagglutinating protein (MoL) from Moringa oleifera seed, and investigated its hemolytic activity. Molecular weight and stability of MoL were also determined. Modification of some amino acid residues was carried out and the effect on MoL hemagglutinating activity determined. Other investigated parameters are the effects of temperature, concentration, incubation period, pH, and sugars on the protein's hemagglutinating and hemolytic activities. The native and subunit molecular weights were estimated as 30 and 27.5 kDa respectively. Hemagglutinating activity of MoL was slightly inhibited by fructose and sucrose, stable at temperature up to 90°C and within pH range of 2-4. Modification of tryptophan and arginine residues resulted in partial loss of hemagglutinating activity. The hemolytic activity of MoL was concentration, temperature, pH, and time-dependent. The study concluded that MoL showed hemolytic (membrane-perturbing) activity in moderate acidic conditions. This suggests its potential exploitation in improved intracellular delivery of bioactive compounds.

Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions

The biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte–TMAO (trimethylamine N-oxide) and destabilizing osmolyte–urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide) and diglycine, by means of FTIR spectroscopy and molecular dynamics simulations. We isolated the spectroscopic share of water molecules that are simultaneously under the influence of peptide and osmolyte and determined the structural and energetic properties of these water molecules. Our experimental and computational results revealed that the changes in the structure of water around peptides, caused by the presence of stabilizing or destabilizing osmolyte, are significantly different for both NAGMA and diglycine. The main factor determining the influence of osmolytes on peptides is the structural-energetic similarity of their hydration spheres. We showed that the chosen peptides can serve as models for various fragments of the protein surface: NAGMA for the protein backbone and diglycine for the protein surface with polar side chains.

Atomic view of cosolute-induced protein denaturation probed by NMR solvent paramagnetic relaxation enhancement

The cosolvent effect arises from the interaction of cosolute molecules with a protein and alters the equilibrium between native and unfolded states. Denaturants shift the equilibrium toward the latter, while osmolytes stabilize the former. The molecular mechanism whereby cosolutes perturb protein stability is still the subject of considerable debate. Probing the molecular details of the cosolvent effect is experimentally challenging as the interactions are very weak and transient, rendering them invisible to most conventional biophysical techniques. Here, we probe cosolute-protein interactions by means of NMR solvent paramagnetic relaxation enhancement together with a formalism we recently developed to quantitatively describe, at atomic resolution, the energetics and dynamics of cosolute-protein interactions in terms of a concentration normalized equilibrium average of the interspin distance, [Formula: see text], and an effective correlation time, τ_c The system studied is the metastable drkN SH3 domain, which exists in dynamic equilibrium between native and unfolded states, thereby permitting us to probe the interactions of cosolutes with both states simultaneously under the same conditions. Two paramagnetic cosolute denaturants were investigated, one neutral and the other negatively charged, differing in the presence of a carboxyamide group versus a carboxylate. Our results demonstrate that attractive cosolute-protein backbone interactions occur largely in the unfolded state and some loop regions in the native state, electrostatic interactions reduce the [Formula: see text] values, and temperature predominantly impacts interactions with the unfolded state. Thus, destabilization of the native state in this instance arises predominantly as a consequence of interactions of the cosolutes with the unfolded state.

Optimized expression and purification of a soluble BMP2 variant based on in-silico design

Bone morphogenetic protein 2 (BMP2¹) is a highly interesting therapeutic growth factor due to its strong osteogenic/osteoinductive potential. However, its pronounced aggregation tendency renders recombinant and soluble production troublesome and complex. While prokaryotic expression systems can provide BMP2 in large amounts, the typically insoluble protein requires complex denaturation-renaturation procedures with medically hazardous reagents to obtain natively folded homodimeric BMP2. Based on a detailed aggregation analysis of wildtype BMP2, we designed a hydrophilic variant of BMP2 additionally containing an improved heparin binding site (BMP2-2Hep-7M). Consecutive optimization of BMP2-2Hep-7M expression and purification enabled production of soluble dimeric BMP2-2Hep-7M in high yield in E. coli. This was achieved by a) increasing protein hydrophilicity via introducing seven point mutations within aggregation hot spots of wildtype BMP2 and a longer N-terminus resulting in higher affinity for heparin, b) by employing E. coli strain SHuffle® T7, which enables the structurally essential disulfide-bond formation in BMP2 in the cytoplasm, c) by using BMP2 variant characteristic soluble expression conditions and application of l-arginine as solubility enhancer. The BMP2 variant BMP2-2Hep-7M shows strongly attenuated although not completely eliminated aggregation tendency.

Effects of Ionic Liquids on Aqueous Urea Solutions: Insights into the Ionic Liquid-Assisted Protein Renaturation

Ionic liquids (ILs) are designer solvents that find wide applications in various areas. Recently, ILs have been shown to induce the refolding of certain proteins that were previously denatured under the treatment of urea. A molecular-level understanding of the counteracting mechanism of ILs on urea-induced protein denaturation remains elusive. In this study, we employ atomistic molecular dynamics simulations to investigate the ternary urea-water-IL solution in comparison to the aqueous urea solution to understand how the presence of ILs can modulate the structure, energetics, and dynamics of urea-water solutions. Our results show that the ions of the IL used, ethylammonium nitrate (EAN), interact strongly with urea and disrupt the urea aggregates that were known to stabilize the unfolded state of the proteins. Results also suggest a disruption in urea-water interaction that releases more free water molecules in solution. We subsequently strengthened these findings by simulating a model peptide in the absence and presence of EAN, which showed broken versus intact secondary structure in urea solution. Analyses show that these changes were accomplished by the added IL, which enforced a gradual displacement of urea from the peptide surface by water. We propose that the ILs facilitate protein renaturation by breaking down the urea aggregates and increasing the amount of free water molecules around the protein.

Interaction strength of osmolytes with the anion of a salt-bridge determines its stability

In order to understand the role of osmolytes in regulating physicochemical behavior of proteins, we investigated the influence of protein destabilizing (urea and guanidinium chloride) and stabilizing osmolytes (TMAO, glycerol, and betaine) on a model salt-bridge (SB) formed between structural analogues of arginine and glutamate/aspartate sidechains in a solvent continuum using first-principles quantum chemical calculations based on DFT and MP2 methods. The binding strength of the osmolyte with the SB is found to be in the order of betaine > TMAO > Gdm+ > glycerol > urea. The osmolytes (TMAO and betaine) that preferentially bind to the SB cation have a marginal influence on SB stability. Also, pure π-π stacking interaction between Gdm+ and the SB cation plays an insignificant role in destabilizing the SB. In fact, the interaction strength of osmolytes with the SB anion mainly determines the stability of SB. For instance, a competition between Gdm+ and the SB cation to bind with the SB anion is responsible for instability and subsequent dissociation of the SB. The competition provided by other osmolytes is too weak to break the SB. Exploiting this information, we designed three structural derivatives of Gdm+, all having a stronger interaction with SB anion, and thereby show a stronger SB dissociation potential. Furthermore, we find an excellent linear anti-correlation between SB interaction energy and the energy of interaction between osmolyte and the SB anion, which suggests that by knowing only the strength of osmolyteacetate interaction, one can predict the influence of osmolytes on the salt-bridge instability. This information is useful in fine-tuning the SB dissociation power of Gdm+, which has a practical significance in obtaining the mechanistic insight into the influence of GdmCl on protein stability. Our results also provide a basis for understanding the chemistry of other ion-pairs formed between a cationic hydrogen donor and an anionic acceptor.

Combined Effects of Methylated Cytosine and Molecular Crowding on the Thermodynamic Stability of DNA Duplexes

Methylated cytosine within CpG dinucleotides is a key factor for epigenetic gene regulation. It has been revealed that methylated cytosine decreases DNA backbone flexibility and increases the thermal stability of DNA. Although the molecular environment is an important factor for the structure, thermodynamics, and function of biomolecules, there are few reports on the effects of methylated cytosine under a cell-mimicking molecular environment. Here, we systematically investigated the effects of methylated cytosine on the thermodynamics of DNA duplexes under molecular crowding conditions, which is a critical difference between the molecular environment in cells and test tubes. Thermodynamic parameters quantitatively demonstrated that the methylation effect and molecular crowding effect on DNA duplexes are independent and additive, in which the degree of the stabilization is the sum of the methylation effect and molecular crowding effect. Furthermore, the effects of methylation and molecular crowding correlate with the hydration states of DNA duplexes. The stabilization effect of methylation was due to the favorable enthalpic contribution, suggesting that direct interactions of the methyl group with adjacent bases and adjacent methyl groups play a role in determining the flexibility and thermodynamics of DNA duplexes. These results are useful to predict the properties of DNA duplexes with methylation in cell-mimicking conditions.

Recent Advances in Hyperthermia Therapy-Based Synergistic Immunotherapy

The past decades have witnessed hyperthermia therapy (HTT) as an emerging strategy against malignant tumors. Nanomaterial-based photothermal therapy (PTT) and magnetic hyperthermia (MHT), as highly effective and noninvasive treatment models, offer advantages over other strategies in the treatment of different types of tumors. However, both PTT and MHT cannot completely cure cancer due to recurrence and distal metastasis. In recent years, cancer immunotherapy has attracted widespread attention owing to its capability to activate the body's own natural defense to identify, attack, and eradicate cancer cells. Significant efforts have been devoted to studying the activated immune responses caused by hyperthermia-ablated tumors. In this article, the synergistic mechanism of HTT in immunotherapy, including immunogenic cell death and reversal of the immunosuppressive tumor microenvironment is discussed. The reports of the combination of HTT or HTT-based multimodal therapy with immunotherapy, including immunoadjuvant exploitation, immune checkpoint blockade therapy, and adoptive cellular immunotherapy are summarized. As highlighted, these strategies could achieve synergistically enhanced therapeutic outcomes against both primary tumors and metastatic lesions, prevent cancer recurrence, and prolong the survival period. Finally, current challenges and prospective developments in HTT-synergized immunotherapy are also reviewed.

Effect of TMAO and Urea on Dimers and Tetramers of Amyloidogenic Heptapeptides (23FGAILSS29)

Human islet amyloid polypeptide (hIAPP) (1-37) is an intrinsically disordered protein that is released with insulin by β-cells found in the pancreas. Under certain environmental conditions, hIAPP can aggregate, which leads to β-cell death. FGAILSS (23-29) residues of the hIAPP protein form β sheets, which may be toxic species in type 2 diabetes (T2D) patients. All-atom molecular dynamics (MD) simulations have been used to analyze the effect of two distinct types of osmolytes trimethylamine N-oxide (TMAO) and urea on two and four FGAILSS heptapeptides. TMAO leads the individual peptide toward an extended conformation with a higher radius of gyration and favors the formation of antiparallel β-sheets with an increase in its concentration. However, urea mostly shows compaction of individual peptides except at 4.0 M in the case of a tetramer but does not show aggregation behavior as a whole. TMAO leads both the dimer and tetramer toward the native state with an increase in its concentration. Moreover, both the dimer and tetramer show irregular behavior in urea. The tetramer in 4.0 M urea shows the maximum fraction of native contacts due to the formation of antiparallel β-sheets. This formation of antiparallel β-sheets favors the aggregation of peptides. TMAO forms a smaller number of hydrogen bonds with peptides as compared to urea as the exclusion of TMAO and accumulation of urea around the peptides have occurred in the first solvation shell (FSS). Principal component analysis (PCA) results suggest that the minima in the free energy landscape (FEL) plot are homogeneous for a particular conformation in TMAO with smaller basins, while in urea, the dimer shows minima mostly for extended conformations. For a 4.0 M urea concentration, the tetramer shows the minimum for antiparallel β-sheets, which indicates the aggregation behavior of the tetramer, and for a higher concentration, it shows minima with wider basins of extended conformations.

Conformational dynamics of superoxide dismutase (SOD1) in osmolytes: a molecular dynamics simulation study

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease caused by the misfolding of Cu, Zn superoxide dismutase (SOD1). Several earlier studies have shown that monomeric apo SOD1 undergoes significant local unfolding dynamics and is the predecessor for aggregation. Here, we have employed atomistic molecular dynamics (MD) simulations to study the structure and dynamics of monomeric apo and holo SOD1 in water, aqueous urea and aqueous urea-TMAO (trimethylamine oxide) solutions. Loop IV (zinc-binding loop) and loop VII (electrostatic loop) of holo SOD1 are considered as functionally important loops as they are responsible for the structural stability of holo SOD1. We found larger local unfolding of loop IV and VII of apo SOD1 as compared to holo SOD1 in water. Urea induced more unfolding in holo SOD1 than apo SOD1, whereas the stabilization of both the form of SOD1 was observed in ternary solution (i.e. water/urea/TMAO solution) but the extent of stabilization was higher in holo SOD1 than apo SOD1. The partially unfolded structures of apo SOD1 in water, urea and holo SOD1 in urea were identified by the exposure of the hydrophobic cores, which are highly dynamic and these may be the initial events of aggregation in SOD1. Our simulation studies support the formation of aggregates by means of the local unfolding of monomeric apo SOD1 as compared to holo SOD1 in water.

Quantitative Interpretation of Solvent Paramagnetic Relaxation for Probing Protein-Cosolute Interactions

Protein-small cosolute molecule interactions are ubiquitous and known to modulate the solubility, stability, and function of many proteins. Characterization of such transient weak interactions at atomic resolution remains challenging. In this work, we develop a simple and practical NMR method for extracting both energetic and dynamic information on protein-cosolute interactions from solvent paramagnetic relaxation enhancement (sPRE) measurements. Our procedure is based on an approximate (non-Lorentzian) spectral density that behaves exactly at both high and low frequencies. This spectral density contains two parameters, one global related to the translational diffusion coefficient of the paramagnetic cosolute, and the other residue specific. These parameters can be readily determined from sPRE data, and then used to calculate analytically a concentration normalized equilibrium average of the interspin distance, ⟨r^-6⟩_norm, and an effective correlation time, τ_C, that provide measures of the energetics and dynamics of the interaction at atomic resolution. We compare our approach with existing ones, and demonstrate the utility of our method using experimental ¹H longitudinal and transverse sPRE data recorded on the protein ubiquitin in the presence of two different nitroxide radical cosolutes, at multiple static magnetic fields. The approach for analyzing sPRE data outlined here provides a powerful tool for deepening our understanding of extremely weak protein-cosolute interactions.

Surface hydration and preferential interaction directs the charged amino acids-induced changes in protein stability

In the present study, we investigate the interaction of amino acid osmolytes, Arg, Lys, Asp and Glu, and a denaturant, guanidinium chloride (Gdm) with proteins. To achieve this, molecular dynamics (MD) simulation of RNase A and α-lactalbumin was performed in the presence of three charged amino acids Arg, Lys, and Asp and the molecular mechanism of amino acid-induced (de)stabilization of the proteins was examined by combining with our earlier report on Glu. As Arg has the side chain similar to that of Gdm and destabilizes the proteins, MD simulation was carried out in the presence of Gdm as well. Radial distribution function and hydration fraction around the protein surface reveals that preferential hydration increases upon the addition of any of the cosolvent; however, the extent of increase is more in the presence of stabilizing cosolvents (stAAs: Lys, Asp and Glu) compared to destabilizing cosolvents (Arg and Gdm). Moreover, the preferential interaction of Arg and Gdm with the proteins is higher than that of stAAs. Residue-level interaction analysis suggests that stAAs preferably interacts with charged amino acids of the proteins whereas Arg and Gdm interactions could be found on almost all the surface exposed residues which might provide higher preferential interaction for these residues. From the results, we propose that the net outcome of preferential hydration versus preferential interaction of the amino acids might determine their effect on the stability of proteins.