Influence of urea and guanidine hydrochloride on lysozyme stability and thermal denaturation; a correlation between activity, protein dynamics and conformational changes

Proteomics Methodologies: The Search of Protein Biomarkers Using Microfluidic Systems Coupled to Mass Spectrometry

Protein biomarkers have been the subject of intensive studies as a target for disease diagnostics and monitoring. Indeed, biomarkers have been extensively used for personalized medicine. In biological samples, these biomarkers are most often present in low concentrations masked by a biologically complex proteome (e.g., blood) making their detection difficult. This complexity is further increased by the needs to detect proteoforms and proteome complexity such as the dynamic range of compound concentrations. The development of techniques that simultaneously pre-concentrate and identify low-abundance biomarkers in these proteomes constitutes an avant-garde approach to the early detection of pathologies. Chromatographic-based methods are widely used for protein separation, but these methods are not adapted for biomarker discovery, as they require complex sample handling due to the low biomarker concentration. Therefore, microfluidics devices have emerged as a technology to overcome these shortcomings. In terms of detection, mass spectrometry (MS) is the standard analytical tool given its high sensitivity and specificity. However, for MS, the biomarker must be introduced as pure as possible in order to avoid chemical noise and improve sensitivity. As a result, microfluidics coupled with MS has become increasingly popular in the field of biomarker discovery. This review will show the different approaches to protein enrichment using miniaturized devices and the importance of their coupling with MS.

Protein Stability─Analysis of Heat and Cold Denaturation without and with Unfolding Models

Protein stability is important in many areas of life sciences. Thermal protein unfolding is investigated extensively with various spectroscopic techniques. The extraction of thermodynamic properties from these measurements requires the application of models. Differential scanning calorimetry (DSC) is less common, but is unique as it measures directly a thermodynamic property, that is, the heat capacity C_p(T). The analysis of C_p(T) is usually performed with the chemical equilibrium two-state model. This is not necessary and leads to incorrect thermodynamic consequences. Here we demonstrate a straightforward model-independent evaluation of heat capacity experiments in terms of protein unfolding enthalpy ΔH(T), entropy ΔS(T), and free energy ΔG(T)). This now allows the comparison of the experimental thermodynamic data with the predictions of different models. We critically examined the standard chemical equilibrium two-state model, which predicts a positive free energy for the native protein, and diverges distinctly from the experimental temperature profiles. We propose two new models which are equally applicable to spectroscopy and calorimetry. The Θ_U(T)-weighted chemical equilibrium model and the statistical-mechanical two-state model provide excellent fits of the experimental data. They predict sigmoidal temperature profiles for enthalpy and entropy, and a trapezoidal temperature profile for the free energy. This is illustrated with experimental examples for heat and cold denaturation of lysozyme and β-lactoglobulin. We then show that the free energy is not a good criterion to judge protein stability. More useful parameters are discussed, including protein cooperativity. The new parameters are embedded in a well-defined thermodynamic context and are amenable to molecular dynamics calculations.

Protein Unfolding—Thermodynamic Perspectives and Unfolding Models

We review the key steps leading to an improved analysis of thermal protein unfolding. Thermal unfolding is a dynamic cooperative process with many short-lived intermediates. Protein unfolding has been measured by various spectroscopic techniques that reveal structural changes, and by differential scanning calorimetry (DSC) that provides the heat capacity change Cp(T). The corresponding temperature profiles of enthalpy ΔH(T), entropy ΔS(T), and free energy ΔG(T) have thus far been evaluated using a chemical equilibrium two-state model. Taking a different approach, we demonstrated that the temperature profiles of enthalpy ΔH(T), entropy ΔS(T), and free energy ΔG(T) can be obtained directly by a numerical integration of the heat capacity profile Cp(T). DSC thus offers the unique possibility to assess these parameters without resorting to a model. These experimental parameters now allow us to examine the predictions of different unfolding models. The standard two-state model fits the experimental heat capacity peak quite well. However, neither the enthalpy nor entropy profiles (predicted to be almost linear) are congruent with the measured sigmoidal temperature profiles, nor is the parabolic free energy profile congruent with the experimentally observed trapezoidal temperature profile. We introduce three new models, an empirical two-state model, a statistical–mechanical two-state model and a cooperative statistical-mechanical multistate model. The empirical model partially corrects for the deficits of the standard model. However, only the two statistical–mechanical models are thermodynamically consistent. The two-state models yield good fits for the enthalpy, entropy and free energy of unfolding of small proteins. The cooperative statistical–mechanical multistate model yields perfect fits, even for the unfolding of large proteins such as antibodies.

Refolding in the modern biopharmaceutical industry

Inclusion bodies (IBs) often emerge upon overexpression of recombinant proteins in E. coli. From IBs, refolding is necessary to generate the native protein that can be further purified to obtain pure and active biologicals. This work focusses on refolding as a significant process step during biopharmaceutical manufacturing with an industrial perspective. A theoretical and historical background on protein refolding gives the reader a starting point for further insights into industrial process development. Quality requirements on IBs as starting material for refolding are discussed and further economic and ecological aspects are considered with regards to buffer systems and refolding conditions. A process development roadmap shows the development of a refolding process starting from first exploratory screening rounds to scale-up and implementation in manufacturing plant. Different aspects, with a direct influence on yield, such as the selection of chemicals including pH, ionic strength, additives, etc., and other often neglected aspects, important during scale-up, such as mixing, and gas-fluid interaction, are highlighted with the use of a quality by design (QbD) approach. The benefits of simulation sciences (process simulation and computer fluid dynamics) and process analytical technology (PAT) for seamless process development are emphasized. The work concludes with an outlook on future applications of refolding and highlights open research inquiries.

Unfolded Lipase at Interfaces Studied via Interfacial Dilational Rheology: The Impact of Urea

Unfolding can interrupt the activity of enzymes. Lipase, the enzyme responsible for triglyceride catalysis, can be deactivated by unfolding, which can significantly affect the yield of enzymatic processes in biochemical engineering. Different agents can induce lipase unfolding, among which we study the impact of urea as a strong denaturant. Unfolding weakens the rigidity and stability of globular proteins, thereby changing the viscoelastic properties of the protein adsorbed layers. These changes can be detected and quantified using interfacial dilational rheology. The urea-induced unfolding of lipase destructs its globular structure, making it more flexible. The interfacial tension and viscoelastic moduli of lipase adsorbed layers reduce upon the addition of urea in the range of studied concentrations. The results agree with the theory that, upon unfolding, a distal region of the loop and tail domain forms adjacent to the proximal region of the interface. The exchange of matter between these regions reduces the viscoelasticity of the unfolded lipase adsorbed layers. Additionally, unfolding reduces the rigidity and brittleness of the lipase adsorbed layers: the aged adsorbed layer of native lipase can break upon high-amplitude perturbations of the interfacial area, unlike the case for urea-induced unfolded lipase.

Current understanding and insights towards protein stabilization and activation in deep eutectic solvents as sustainable solvent media

Deep eutectic solvents (DESs) have emerged as a new class of green, designer and biocompatible solvents, an alternative to conventional organic solvents and ionic liquids (ILs) which are comparatively toxic and non-biodegradable. DESs are eutectic mixtures that are formed when a hydrogen bond acceptor (HBA) is mixed with a hydrogen bond donor (HBD) at particular molar ratios by mechanical grinding or under mild heating conditions. Very recently, these solvents have been the center of attention for researchers in biotechnology, biomedicine and various scientific applications. These environmentally benign solvents have a close analogy with ILs; however, they offer certain unique merits over traditional ILs. DESs display remarkable properties such as easy preparation, tunable composition, biodegradability, recyclability, inherently low toxicity, sustainability and biocompatibility; these special features validate DESs as new potential solvents/co-solvents for biomolecules. Mechanistically, the biocompatibility and protein friendly nature of DESs depend on various factors, which include the composition of the DES, viscosity and hydration level. Therefore, it becomes an essential task to bring together all the studies related to protein behaviour in DESs to unlock their biomolecular proficiency. This review specifically highlights recent insights into the biomacromolecular functionality in DESs, including outlines of the solubilization and stabilization of proteins, long term protein packaging, different extraction methods and enzyme activation in the presence of DESs. A literature survey reveals that DESs act as green media in which the protein structure and activity are retained. In some cases, proteins refolded and enzymatic activity was enhanced several fold in the presence of DESs. Furthermore, we have reviewed the possible mechanistic behaviour behind protein stabilization, refolding and activation in DESs. Overall, the main objective of this review is to explicate the advantages of the introduction of DESs for biomolecules and to demonstrate the versatility of these eco-friendly solvents for future bio-based applications.

Influence of Urea and Dimethyl Sulfoxide on K-Peptide Fibrillation

Protein fibrillation leads to formation of amyloids-linear aggregates that are hallmarks of many serious diseases, including Alzheimer's and Parkinson's diseases. In this work, we investigate the fibrillation of a short peptide (K-peptide) from the amyloidogenic core of hen egg white lysozyme in the presence of dimethyl sulfoxide or urea. During the studies, a variety of spectroscopic methods were used: fluorescence spectroscopy and the Thioflavin T assay, circular dichroism, Fourier-transform infrared spectroscopy, optical density measurements, dynamic light scattering and intrinsic fluorescence. Additionally, the presence of amyloids was confirmed by atomic force microscopy. The obtained results show that the K-peptide is highly prone to form fibrillar aggregates. The measurements also confirm the weak impact of dimethyl sulfoxide on peptide fibrillation and distinct influence of urea. We believe that the K-peptide has higher amyloidogenic propensity than the whole protein, i.e., hen egg white lysozyme, most likely due to the lack of the first step of amyloidogenesis-partial unfolding of the native structure. Urea influences the second step of K-peptide amyloidogenesis, i.e., folding into amyloids.

The role of water in the reversibility of thermal denaturation of lysozyme in solid and liquid states

Although unfolding of protein in the liquid state is relatively well studied, its mechanisms in the solid state, are much less understood. We evaluated the reversibility of thermal unfolding of lysozyme with respect to the water content using a combination of thermodynamic and structural techniques such as differential scanning calorimetry, synchrotron small and wide-angle X-ray scattering (SWAXS) and Raman spectroscopy. Analysis of the endothermic thermal transition obtained by DSC scans showed three distinct unfolding behaviors at different water contents. Using SWAXS and Raman spectroscopy, we investigated reversibility of the unfolding for each hydration regime for various structural levels including overall molecular shape, secondary structure, hydrophobic and hydrogen bonding interactions. In the substantially dehydrated state below 37 wt% of water the unfolding is an irreversible process and can be described by a kinetic approach; above 60 wt% the process is reversible, and the thermodynamic equilibrium approach is applied. In the intermediate range of water contents between 37 wt% and 60 wt%, the system is phase separated and the thermal denaturation involves two processes: melting of protein crystals and unfolding of protein molecules. A phase diagram of thermal unfolding/denaturation in lysozyme - water system was constructed based on the experimental data.

•

Denaturation of lysozyme in solid and liquid is studied using SAXS, Raman and DSC.

•

Denaturation of lysozyme in liquid is reversible, in solid state it is irreversible.

•

A phase diagram of lysozyme-water system is constructed.

Functional-State Dependence of Picosecond Protein Dynamics

We examine temperature-dependent picosecond dynamics of two benchmarking proteins lysozyme and cytochrome c using temperature-dependent terahertz permittivity measurements. We find that a double Arrhenius temperature dependence with activation energies E₁ ∼ 0.1 kJ/mol and E₂ ∼ 10 kJ/mol fits the folded and ligand-free state response. The higher activation energy is consistent with the so-called protein dynamical transition associated with beta relaxations at the solvent-protein interface. The lower activation energy is consistent with correlated structural motions. When the structure is removed by denaturing, the lower-activation-energy process is no longer present. Additionally, the lower-activation-energy process is diminished with ligand binding but not for changes in the internal oxidation state. We suggest that the lower-energy activation process is associated with collective structural motions that are no longer accessible with denaturing or binding.

Impact of denaturing agents on surface properties of myoglobin solutions

The addition of denaturants strongly influences the surface properties of aqueous myoglobin solutions. The effect differs from the results for mixed solutions of the denaturants and other globular proteins, for example, bovine serum albumin (BSA), lysozyme and β-lactoglobulin (BLG), although the surface properties of the solutions of the pure proteins are similar. The kinetic dependencies of the dynamic surface elasticity of myoglobin solutions with guanidine hydrochloride (GuHCl) reveal at least two adsorption steps at denaturant concentrations higher than 1 M: a very fast increase of the dynamic surface elasticity to approximately 30 mN/m at the beginning of adsorption, and a slower growth to abnormally high values of 250-300 mN/m. At the same time, the surface elasticity of BSA/GuHCl, BLG/GuHCl and lysozyme/GuHCl solutions is a non-monotonic function of the surface age, and does not exceed 50 mN/m close to equilibrium. The high surface elasticity of myoglobin/GuHCl solutions may be associated with protein aggregation in the surface layer. The formation of aggregates is confirmed by ellipsometry and Brewster angle microscopy. The addition of ionic surfactants to protein solutions leads to the formation of myoglobin/surfactant complexes, and the kinetic dependencies of the dynamic surface elasticity display local maxima indicating multistep adsorption kinetics, unlike the corresponding results for solutions of other globular proteins mixed with ionic surfactants. Ellipsometry and infrared reflection-absorption spectroscopy allow tracing the adsorption of the complexes and their displacement from the interface at high surfactant concentrations.

Unfolding and Aggregation of Lysozyme under the Combined Action of Dithiothreitol and Guanidine Hydrochloride: Optical Studies

Using a number of optical techniques (interferometry, dynamic light scattering, and spectroscopy), denaturation of hen egg white lysozyme (HEWL) by treatment with a combination of dithiothreitol (DTT) and guanidine hydrochloride (GdnHCl) has been investigated. The denaturing solutions were selected so that protein denaturation occurred with aggregation (Tris-HCl pH = 8.0, 50 mM, DTT 30 mM) or without aggregation (Tris-HCl pH = 8.0, 50 mM, DTT 30 mM, GdnHCl 6 M) and can be evaluated after 60 min of treatment. It has been found that denatured by solution with 6 M GdnHCl lysozyme completely loses its enzymatic activity after 30 min and the size of the protein molecule increases by 1.5 times, from 3.8 nm to 5.7 nm. Denaturation without of GdnHCl led to aggregation with preserving about 50% of its enzymatic activity. Denaturation of HEWL was examined using interferometry. Previously, it has been shown that protein denaturation that occurs without subsequent aggregation leads to an increase in the refractive index (Δn ~ 4.5 × 10-5). This is most likely due to variations in the HEWL-solvent interface area. By applying modern optical techniques conjointly, it has been possible to obtain information on the nature of time-dependent changes that occur inside a protein and its hydration shell as it undergoes denaturation.

Effect of pH and urea on the proteins secondary structure at the water/air interface and in solution

HYPOTHESIS

The secondary structure of proteins affects their functionality and performance in physiological environments or industrial applications. Change of the solution pH or the presence of protein denaturants are the main chemical means that can alter the secondary structure of proteins or lead to protein denaturation. Since proteins in the bulk solution and those residing at the solution/air interface experience different local environments, their response to chemical denaturation can be different.

EXPERIMENTS

We utilize circular dichroism and chiral/achiral sum frequency generation spectroscopy to study the secondary structure of selected proteins as a function of the solution pH or in the presence of 8 M urea in the bulk solution and at the solution/air interface, respectively.

FINDINGS

The liquid/air interface can enhance or decrease protein conformation stability. The change in the secondary structure of the surface adsorbed proteins in alkaline solutions occurs at pH values lower than those denaturing the studied proteins in the bulk solution. In contrast, while 8 M urea completely denatures the studied proteins in the bulk solution, the liquid/air interface prevents the urea-induced denaturation of the surface adsorbed proteins by limiting the access of urea to the hydrophobic side chains of proteins protruding to air.

Direct involvement of Hsp70 ATP hydrolysis in Ubr1-dependent quality control

Chaperones can mediate both protein folding and degradation. This process is referred to as protein triage, which demands study to reveal mechanisms of quality control for both basic scientific and translational purposes. In yeast, many misfolded proteins undergo chaperone-dependent ubiquitination by the action of the E3 ligases Ubr1 and San1, allowing detailed study of protein triage. In cells, both HSP70 and HSP90 mediated substrate ubiquitination, and the canonical ATP cycle was required for HSP70’s role: we have found that ATP hydrolysis by HSP70, the nucleotide exchange activity of Sse1, and the action of J-proteins are all needed for Ubr1-mediated quality control. To discern whether chaperones were directly involved in Ubr1-mediated ubiquitination, we developed a bead-based assay with covalently immobilized but releasable misfolded protein to obviate possible chaperone effects on substrate physical state or transport. In this in vitro assay, only HSP70 was required, along with its ATPase cycle and relevant cochaperones, for Ubr1-mediated ubiquitination. The requirement for the HSP70 ATP cycle in ubiquitination suggests a possible model of triage in which efficiently folded proteins are spared, while slow-folding or nonfolding proteins are iteratively tagged with ubiquitin for subsequent degradation.

Thermal and Chemical Unfolding of a Monoclonal IgG1 Antibody: Application of the Multistate Zimm-Bragg Theory

The thermal unfolding of a recombinant monoclonal antibody IgG1 (mAb) was measured with differential scanning calorimetry (DSC). The DSC thermograms reveal a pretransition at 72°C with an unfolding enthalpy of ΔH_cal ∼200-300 kcal/mol and a main transition at 85°C with an enthalpy of ∼900-1000 kcal/mol. In contrast to small single-domain proteins, mAb unfolding is a complex reaction that is analyzed with the multistate Zimm-Bragg theory. For the investigated mAb, unfolding is characterized by a cooperativity parameter σ ∼6 × 10^-5 and a Gibbs free energy of unfolding of g_nu ∼100 cal/mol per amino acid. The enthalpy of unfolding provides the number of amino acid residues ν participating in the unfolding reaction. On average, ν∼220 ± 50 amino acids are involved in the pretransition and ν∼850 ± 30 in the main transition, accounting for ∼90% of all amino acids. Thermal unfolding was further studied in the presence of guanidineHCl. The chemical denaturant reduces the unfolding enthalpy ΔH_cal and lowers the midpoint temperature T_m. Both parameters depend linearly on the concentration of denaturant. The guanidineHCl concentrations needed to unfold mAb at 25°C are predicted to be 2-3 M for the pretransition and 5-7 M for the main transition, varying with pH. GuanidineHCl binds to mAb with an exothermic binding enthalpy, which partially compensates the endothermic mAb unfolding enthalpy. The number of guanidineHCl molecules bound upon unfolding is deduced from the DSC thermograms. The bound guanidineHCl-to-unfolded amino acid ratio is 0.79 for the pretransition and 0.55 for the main transition. The pretransition binds more denaturant molecules and is more sensitive to unfolding than the main transition. The current study shows the strength of the Zimm-Bragg theory for the quantitative description of unfolding events of large, therapeutic proteins, such as a monoclonal antibody.

Denaturant effect on amyloid fibrils: Declasterization, depolymerization, denaturation and reassembly

Accumulation of amyloid fibrils in organism accompanies many serious diseases, such as Alzheimer's and Parkinson's diseases, diabetes, prion diseases, etc. It is generally accepted that amyloids are highly resistant to degradation, which complicates their elimination in vivo and is one of the reasons for their pathogenicity. However, using a wide range of physicochemical approaches and specially elaborated method for the tested samples preparation by equilibrium microdialysis technique, it is proved that the stability of amyloids is greatly exaggerated. It turned out that amyloid fibrils formed from at least two amyloidogenic proteins, one of which is a model object for fibrils studying and the second is the cause of hemodialysis amyloidosis in an acute renal failure, are less stable than monomeric proteins. A mechanism of the degradation/reassembly of amyloid fibrils was proposed. It was shown that amyloid «seed» is a factor affecting not only the rate of the fibrils formation, but also their structure. Obtained results are a step towards identifying effects that can lead to degradation of amyloids and their clearance without adverse influence on the functionally active state of the protein or to change the structure and, as a result, the pathogenicity of these protein aggregates.

Thermal and Chemical Unfolding of Lysozyme. Multistate Zimm-Bragg Theory Versus Two-State Model

Thermal and chemical unfolding of lysozyme in the presence of the guanidine HCl denaturant is a model system to compare the conventional two-state model of protein unfolding with the multistate Zimm-Bragg theory. The two-state model is shown to be the noncooperative limit of the Zimm-Bragg theory. In particular, the Zimm-Bragg theory provides a molecular interpretation of the empirical linear extrapolation method (LEM) of the two-state model. Differential scanning calorimetry (DSC) experiments reported in the literature are analyzed with both methods. Lysozyme unfolding is associated with a large endothermic enthalpy that decreases significantly upon addition of guanidine HCl. In contrast, the Gibbs free energy of unfolding is small, negative, and independent of the guanidine HCl concentration, contradicting, in part, the conclusions of the LEM. The unfolding enthalpy is compensated by an even larger entropy term. The multistate Zimm-Bragg theory predicts a larger conformational enthalpy and a smaller Gibbs free energy than the two-state model. The Zimm-Bragg theory provides the protein cooperativity parameter, the average length of independently folding protein domains, and the Gibbs free energy of unfolding of individual amino acid residues. Guanidine HCl binding to lysozyme is exothermic and counteracts the endothermic unfolding enthalpy. The number of bound denaturant molecules is determined from the decrease in enthalpy and is extrapolated to the guanidine HCl-to-amino acid stoichiometry at complete lysozyme unfolding. Chemical unfolding isotherms measured with circular dichroism (CD) spectroscopy are analyzed with both models. The chemical Zimm-Bragg theory is a cooperative molecular model, yielding the guanidine HCl binding constant and the protein cooperativity parameter. It allows a quantitative comparison between thermal and chemical protein unfolding. The two reactions have almost identical changes in Gibbs free energy. However, thermal unfolding is significantly more cooperative than chemical unfolding. Finally, distinct differences are observed in thermal unfolding between DSC and CD spectroscopy.

The Effect of Dimethyl Sulfoxide on the Lysozyme Unfolding Kinetics, Thermodynamics, and Mechanism

The thermal stability of proteins in the presence of organic solvents and the search for ways to increase this stability are important topics in industrial biocatalysis and protein engineering. The denaturation of hen egg-white lysozyme in mixtures of water with dimethyl sulfoxide (DMSO) with a broad range of compositions was studied using a combination of differential scanning calorimetry (DSC), circular dichroism (CD), and spectrofluorimetry techniques. In this study, for the first time, the kinetics of unfolding of lysozyme in DMSO–water mixtures was characterized. In the presence of DMSO, a sharp decrease in near-UV CD and an increase in the fluorescence signal were observed at lower temperatures than the DSC denaturation peak. It was found that differences in the temperatures of the CD and DSC signal changes increase as the content of DMSO increases. Changes in CD and fluorescence are triggered by a break of the tertiary contacts, leading to an intermediate state, while the DSC peak corresponds to a subsequent complete loss of the native structure. In this way, the commonly used two-state model was proven to be unsuitable to describe the unfolding of lysozyme in the presence of DMSO. In kinetic studies, it was found that even high concentrations of DMSO do not drastically change the activation energy of the initial stage of unfolding associated with a disruption of the tertiary structure, while the enthalpy of denaturation shows a significant dependence on DMSO content. This observation suggests that the structure of the transition state upon unfolding remains similar to the structure of the native state.

Monitoring of lysozyme thermal denaturation by volumetric measurements and nanoDSF technique in the presence of N-butylurea

The results of thermal studies of denaturation of hen egg white lysozyme (HEWL) in water and an aqueous solution of N-butylurea (BU) are presented. High-precision densimetric measurements were used to characterize and analyze the changes of the specific volume, v, during temperature elevation. The temperature of the midpoint of protein denaturation was also determined by nanoDSF technique (differential scanning fluorimetry). The densities of lysozyme solutions were measured at temperatures ranging from 298.15 to 353.15 K with an interval of 5 K at atmospheric pressure (0.1 MPa). The concentration of the protein covered the range from 2 to 20 mg per 1 ml of the solution. The optimal range of the concentration for the densimetric measurements was roughly estimated. In the transition region, the structural changes of the protein are accompanied by the biggest increase of ν values with temperature. Our measurements show that this effect can be monitored from volumetric data without precise determination of protein concentration. The results prove that a two-state model of denaturation could be used for data interpretation. Contrary to common misconception, the volumetric measurements suggest that the denatured protein does not necessarily need to be in a fully extended state. In this way, the 'protein volume paradox' could be explained. The surface area of the protein remains unchanged and thus the increase of the specific volume of the protein is relatively small. Additionally, the self-stabilizing effect of the protein in BU solution was reported. For the HEWL in pure water, this phenomenon was not observed.

Uncovering dehydration in cytochrome c refolding from urea- and guanidine hydrochloride-denatured unfolded state by high pressure spectroscopy

To investigate the dehydration associated with protein folding, the partial molar volume changes for protein unfolding (ΔV_u) in cytochrome c (Cyt c) were determined using high pressure absorption spectroscopy. ΔV_u values for the unfolding to urea- and guanidine hydrochloride (GdnHCl)-denatured Cyt c were estimated to be 56±5 and 29±1 mL mol⁻¹, respectively. Considering that the volume change for hydration of hydrophobic groups is positive and that Cyt c has a covalently bonded heme, a positive ΔV_u reflects the primary contribution of the hydration of heme. Because of the marked tendency of guanidium ions to interact with hydrophobic groups, a smaller number of water molecules were hydrated with hydrophobic groups in GdnHCl-denatured Cyt c than in urea-denatured Cyt c, resulting in the smaller positive ΔV_u. On the other hand, urea is a relatively weak denaturant and urea-denatured Cyt c is not completely hydrated, which retains the partially folded structures. To unfold such partial structures, we introduced a mutation near the heme binding site, His26, to Gln, resulting in a negatively shifted ΔV_u (4±2 mL mol⁻¹) in urea-denatured Cyt c. The formation of the more solvated and less structured state in the urea-denatured mutant enhanced hydration to the hydrophilic groups in the unfolding process. Therefore, we confirmed the hydration of amino acid residues in the protein unfolding of Cyt c by estimating ΔV_u, which allows us to discuss the hydrated structures in the denatured states of proteins.

Detecting lysozyme unfolding via the fluorescence of lysozyme encapsulated gold nanoclusters

Protein misfolding plays a critical role in the manifestation of amyloidosis type diseases. Therefore, understanding protein unfolding and the ability to track protein unfolding in a dynamic manner are of considerable interest. Fluorescence-based techniques are powerful tools for gaining real-time information about the local environmental conditions of a probe on the nanoscale. Fluorescent gold nanoclusters (AuNCs) are a new type of fluorescent probes which are <2 nm in diameter, incredibly robust and offer highly sensitive, wavelength tuneable emission. Their small size minimises intrusion and makes AuNCs ideal for studying protein dynamics. Lysozyme has previously been used to encapsulate AuNCs. The unfolding dynamics of lysozyme under different environmental conditions have been well-studied and being an amyloid type protein makes lysozyme an ideal candidate for encapsulating AuNCs in order to test their sensitivity to protein unfolding. In this study, we tracked the fluorescence characteristics of AuNCs encapsulated in lysozyme while inducing protein unfolding using urea, sodium dodecyl sulphate (SDS) and elevated temperature and compared them to complimentary circular dichroism spectra. It is found that AuNC fluorescence emission is quenched upon induced protein unfolding either due to a decrease in Forster Resonance Energy Transfer (FRET) efficiency between tryptophan and AuNCs or solvent exposure of the AuNC. Fluorescence lifetime measurements confirmed quenching to be collisional via oxygen dissolved in a solution which increases as the AuNC was exposed to the solvent during unfolding. Moreover, the longer decay component τ₁ was observed to decrease as the protein unfolded, due to the increased collisional quenching. It is suggested that AuNC sensitivity to solvent exposure might be utilised in the future as a new approach to studying and possibly even detecting amyloidosis type diseases.

Effect of Weakly Interacting Cosolutes on Lysozyme Conformations

Exposure of a protein to cosolutes, like denaturants, changes its folding equilibrium. To determine the ensemble of protein conformations at equilibrium, in the presence of weakly interacting cosolutes, we present a two-stage analysis of solution X-ray scattering data. In the first stage, Guinier analysis and Kratky plot revealed information about the compactness and flexibility of the protein. In the second stage, elastic network contact model and coarse-grained normal mode analysis were used to generate an ensemble of conformations. The scattering curves of the conformations were computed and fitted to the measured scattering curves to get insights into the dominating folding states at equilibrium. Urea and guanidine hydrochloride (GuHCl) behaved as preferentially included weakly interacting cosolutes and induced denaturation of hen egg-white lysozyme, which served as our test case. The computed models adequately fit the data and gave ensembles of conformations that were consistent with our measurements. The analysis suggests that in the presence of urea, lysozyme retained its compactness and assumed molten globule characteristics, whereas in the presence of GuHCl lysozyme adopted random coiled conformations. Interestingly, no equilibrium intermediate states were observed in both urea and GuHCl.

X-ray crystallographic analysis of time-dependent binding of guanidine hydrochloride to HEWL: First steps during protein unfolding

Time-dependent binding of guanidine hydrochloride (GuHCl) to hen egg-white lysozyme (HEWL), and effects of this binding on the protein structure have been investigated by solving X-ray structures of crystalline complexes. The complexes have been prepared by soaking, for different periods of time, native lysozyme crystals in solutions containing 2.5M GuHCl. In the refined structures, the number of water molecules in the protein's first solvent shell has progressively decreased from 152 to 115, showing protein's preference for guanidinium over water. Guanidinium ions preferentially hydrogen bond with the backbone carbonyl oxygen atoms. In their van der Waals interactions, they do not show any preference for apolar residues. Guanidinium ions have replaced water molecules that form cages around exposed hydrophobic residues. Guanidinium binding has decreased the average length of water-water hydrogen bond by 0.1Å. The hydrogen bonds between main chain atoms have been weakened by GuHCl, and this may be the reason for increased potency of GuHCl compared to urea. Guanidinium binding destabilizes the β-domain by causing loss of hydrogen bonds involving Asn 59 side chain. Interestingly, this loss is almost identical to that observed in structures of amyloidogenic variants of human lysozyme. Compounds preventing this loss could be anti-amyloidogenic.

Contrasting Effects of Guanidinium Chloride and Urea on the Activity and Unfolding of Lysozyme

Cosolvents play an important role in regulating the stability and function of proteins present in the cell. We studied the role of cosolvents, urea and guanidinium chloride (GdmCl), which act as protein denaturants, in the catalytic activity and structural stability of the protein lysozyme using activity measurements, spectroscopy, and molecular dynamics simulations. We find that the activity of lysozyme increases on the addition of urea, whereas it decreases sharply on the addition of GdmCl. At low GdmCl concentrations ([GdmCl] < 4 M), the activity of lysozyme decreases, even though there is no significant perturbation in the structure of the lysozyme folded state. We find that this is due to the strong interaction of the Gdm⁺ ion with the residues Asp52 and Glu35, which are present in the lysozyme catalytic site. In contrast, urea interacts with Trp63 present in the loop region present near the active site of lysozyme, inducing minor conformational changes in lysozyme, which can increase the activity of lysozyme. At higher denaturant concentrations, experiments show that GdmCl completely denatures the protein, whereas the folded state is stable in the presence of urea. We further show that GdmCl denatures lysozyme with the disulfide bonds intact in the protein, whereas urea denatures the protein only when the disulfide bonds are broken using reducing agents.

Adsorption of Denaturated Lysozyme at the Air-Water Interface: Structure and Morphology

The application of protein deuteration and high flux neutron reflectometry has allowed a comparison of the adsorption properties of lysozyme at the air-water interface from dilute solutions in the absence and presence of high concentrations of two strong denaturants: urea and guanidine hydrochloride (GuHCl). The surface excess and adsorption layer thickness were resolved and complemented by images of the mesoscopic lateral morphology from Brewster angle microscopy. It was revealed that the thickness of the adsorption layer in the absence of added denaturants is less than the short axial length of the lysozyme molecule, which indicates deformation of the globules at the interface. Two-dimensional elongated aggregates in the surface layer merge over time to form an extensive network at the approach to steady state. Addition of denaturants in the bulk results in an acceleration of adsorption and an increase of the adsorption layer thickness. These results are attributed to incomplete collapse of the globules in the bulk from the effects of the denaturants as a result of interactions between remote amino acid residues. Both effects may be connected to an increase of the effective total volume of macromolecules due to the changes of their tertiary structure, that is, the formation of molten globules under the influence of urea and the partial unfolding of globules under the influence of GuHCl. In the former case, the increase of globule hydrophobicity leads to cooperative aggregation in the surface layer during adsorption. Unlike in the case of solutions without denaturants, the surface aggregates are short and wormlike, their size does not change with time, and they do not merge to form an extensive network at the approach to steady state. To the best of our knowledge, these are the first observations of cooperative aggregation in lysozyme adsorption layers.

Cooperative protein unfolding. A statistical-mechanical model for the action of denaturants

Knowledge of protein stability is of utmost importance in various fields of biotechnology. Protein stability can be assessed in solution by increasing the concentration of denaturant and recording the structural changes with spectroscopic or thermodynamic methods. The standard interpretation of the experimental data is to assume a 2-state equilibrium between completely folded and completely unfolded protein molecules. Here we propose a cooperative model based on the statistical-mechanical Zimm-Bragg theory. In this model protein unfolding is driven by the weak binding of a rather small number of denaturant molecules, inducing the cooperative unfolding with multiple dynamic intermediates. The modified Zimm-Bragg theory is applied to published thermodynamic and spectroscopic data leading to the following conclusions. (i) The binding constant K_D is correlated with the midpoint concentration, c₀, of the unfolding reaction according to c₀≅1/K_D. The better the binding of denaturant the lower is the concentration to achieve unfolding. (ii) The binding constant K_D agrees with direct thermodynamic measurements. A rather small number of bound denaturants suffices to induce the cooperative unfolding of the whole protein. (iii) Chemical unfolding occurs in the concentration range Δc_D=c_end-c_ini. The theory predicts the unfolding energy per amino acid residue as g_nu=RTK_D(c_end-c_ini). The Gibbs free energy of an osmotic gradient of the same size is ΔG_Diff=-RTln(c_end/c_ini). In all examples investigated ΔG_Diff exactly balances the unfolding energy g_nu. The total unfolding energy is thus close to zero. (iv) Protein cooperativity in chemical unfolding is rather low with cooperativity parameters σ≥3x10^-3. As a consequence, the theory predicts a dynamic mixture of conformations during the unfolding reaction. The probabilities of individual conformations are easily accessible via the partition function Z(c_D,σ).

Molecular dynamics study of unfolding of lysozyme in water and its mixtures with dimethyl sulfoxide

All-atom explicit solvent molecular dynamics was used to study the process of unfolding of hen egg white lysozyme in water and mixtures of water with dimethyl sulfoxide at different compositions. We have determined the kinetic parameters of unfolding at a constant temperature 450K. For each run, the time of disruption of the tertiary structure of lysozyme t_u was defined as the moment when a certain structural criterion computed from the trajectory reaches its critical value. A good agreement is observed between the results obtained using several different criteria. The secondary structure according to DSSP calculations is found to be partially unfolded to the moment of disruption of tertiary structure, but some of its elements keep for a long time after that. The values of t_u averaged over ten 30ns-long trajectories for each solvent composition are shown to decrease very rapidly with addition of dimethyl sulfoxide, and rather small amounts of dimethyl sulfoxide are found to change the pathway of unfolding. In pure water, despite the loss of tertiary contacts and disruption of secondary structure elements, the protein preserves its compact globular state at least over 130ns of simulation, while even at 5mol percents of dimethyl sulfoxide it loses its compactness within 30ns. The proposed methodology is a generally applicable tool to quantify the rate of protein unfolding in simulation studies.

Directly Probing Intermolecular Structural Change of a Core Fragment of β2-Microglobulin Amyloid Fibrils with Low-Frequency Raman Spectroscopy

Amyloid fibrils, which are ordered aggregates of proteins or peptides, have attracted keen interest because their deposition causes serious human diseases. Despite many studies utilizing X-ray crystallography, solid-state NMR, and other methods, intermolecular interactions governing the fibril formation remain largely unclear. Here, we used low-frequency Raman (LFR) spectroscopy to investigate the intermolecular β-sheet structure of a core fragment of β₂-microglobulin amyloid fibrils, β₂m_21-29, in aqueous buffer solutions. The LFR spectra (approximately 10-200 cm^-1) of β₂m_21-29 amyloid fibrils measured at different pH values (ranging from 6.8 to 8.0) revealed a broad-spectral pattern with a maximum at ∼80 cm^-1 below pH 7.2 and at ∼110 cm^-1 above pH 7.4. This observation is attributed to a pH-dependent structural change from an antiparallel to a parallel intermolecular β-sheet structure. Multivariate curve resolution-alternating least-squares (MCR-ALS) analysis enabled us to decompose the apparently monotonous LFR spectra into three distinctly different contributions: intermolecular vibrations of the parallel and antiparallel β-sheets and intramolecular vibrations of the peptide backbone. Peak positions of the obtained LFR bands not only exhibit a much more pronounced difference between the two β-sheets than the conventional amide I band, but they also suggest stronger intermolecular interaction, due presumably to the hydrophobic effect, in the parallel β-sheet than in the antiparallel β-sheet. The present results show that LFR spectroscopy in combination with the MCR-ALS analysis holds promise for real-time tracking of the intermolecular dynamics of amyloid fibril formation under physiological conditions.

Activity and stability analysis of covalent conjugated lysozyme-single walled carbon nanotubes: potential biomedical and industrial applications

Analysis of covalent conjugated lysozyme-single walled carbon nanotubes.

Proteins Take up Water Before Unfolding

Proteins perform specific biological functions that strongly depend on their three-dimensional structure. This three-dimensional structure, i.e. the way the protein folds, is strongly determined by the interaction between the protein and the water solvent. We study the dynamics of water in aqueous solutions of several globular proteins at different degrees of urea-induced unfolding, using polarization-resolved femtosecond infrared spectroscopy. We observe that a fraction of the water molecules is strongly slowed down by their interaction with the protein surface. By monitoring the slow water fraction we can directly probe the amount of water-exposed protein surface. We find that at mild denaturing conditions, the water-exposed surface increases by almost 50%, while the secondary structure is still intact. This finding indicates that protein unfolding starts with the protein structure becoming less tight, thereby allowing water to enter.

Recent developments in the Raman and infrared investigations of amorphous pharmaceuticals and protein formulations: A review

The success rate for drug discovery and the development of innovative therapeutic strategies are intimately related to the physical properties of the solid-state condensed matter, which have direct influence on the bioavailability of Active Pharmaceutical Ingredients. In order to transform a new molecule in efficient drug, the material is brought into an amorphous state using various manufacturing processes including freeze drying, spray drying, hot melt extrusion and loading in different delivery devices. The infrared and Raman spectroscopic analyses used for exploring disordered and amorphous states, for the monitoring of the drug physical stability in drug delivery systems are described in this review.

Effects of monohydric alcohols and polyols on the thermal stability of a protein

The thermal stability of a protein is lowered by the addition of a monohydric alcohol, and this effect becomes larger as the size of hydrophobic group in an alcohol molecule increases. By contrast, it is enhanced by the addition of a polyol possessing two or more hydroxyl groups per molecule, and this effect becomes larger as the number of hydroxyl groups increases. Here, we show that all of these experimental observations can be reproduced even in a quantitative sense by rigid-body models focused on the entropic effect originating from the translational displacement of solvent molecules. The solvent is either pure water or water-cosolvent solution. Three monohydric alcohols and five polyols are considered as cosolvents. In the rigid-body models, a protein is a fused hard spheres accounting for the polyatomic structure in the atomic detail, and the solvent is formed by hard spheres or a binary mixture of hard spheres with different diameters. The effective diameter of cosolvent molecules and the packing fractions of water and cosolvent, which are crucially important parameters, are carefully estimated using the experimental data of properties such as the density of solid crystal of cosolvent, parameters in the pertinent cosolvent-cosolvent interaction potential, and density of water-cosolvent solution. We employ the morphometric approach combined with the integral equation theory, which is best suited to the physical interpretation of the calculation result. It is argued that the degree of solvent crowding in the bulk is the key factor. When it is made more serious by the cosolvent addition, the solvent-entropy gain upon protein folding is magnified, leading to the enhanced thermal stability. When it is made less serious, the opposite is true. The mechanism of the effects of monohydric alcohols and polyols is physically the same as that of sugars. However, when the rigid-body models are employed for the effect of urea, its addition is predicted to enhance the thermal stability, which conflicts with the experimental fact. We then propose, as two essential factors, not only the solvent-entropy gain but also the loss of protein-solvent interaction energy upon protein folding. The competition of changes in these two factors induced by the cosolvent addition determines the thermal-stability change.

Refolding effects of partially immiscible ammonium-based ionic liquids on the urea-induced unfolded lysozyme structure

Refolding ability of partially-immiscible ammonium-based ionic liquids on the urea-induced unfolded lysozyme.

Microscopic significance of hydrophobic residues in the protein-stabilizing effect of trimethylamine N-oxide (TMAO)

Proteins with a higher hydrophobic content are better protected by TMAO against the deleterious effect of urea.

Activity and conformation of lysozyme in molecular solvents, protic ionic liquids (PILs) and salt–water systems

The role of solvent features on enzyme stability was investigated by comparing the conformation and activity of lysozyme in molecular solvents, PILs and salt solutions. Electrostatic interactions and the solvophobic effect dominated at low and high solvent concentrations, respectively.

Evaluation of the Effectiveness of Surfactants and Denaturants to Elute and Denature Adsorbed Protein on Different Surface Chemistries

The elution and/or denaturation of proteins from material surfaces by chemical excipients such as surfactants and denaturants is important for numerous applications including medical implant reprocessing, bioanalyses, and biodefense. The objective of this study was to develop and apply methods to quantitatively assess how surface chemistry and adsorption conditions influence the effectiveness of three commonly used surfactants (sodium dodecyl sulfate, n-octyl-β-d-glucoside, and 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate) and two denaturants (guanidium hydrochloride and urea) to elute protein (hen egg white lysozyme and bovine pancreatic ribonuclease A) from three different surface chemistries (silica glass, poly(methyl methacrylate), and high-density polyethylene). The structure and bioactivity of residual protein on the surface following elution were characterized using circular dichroism spectropolarimetry and enzyme assays to assess the extent of protein denaturation. Our results indicate that the denaturants were generally more effective than the surfactants in removing the adsorbed proteins from each type of surface. Also, the denaturing capacity of these excipients on the residual proteins on the surfaces was distinctly different from their influence on the proteins in solution and was unique for each of the adsorption conditions. Taken altogether, these results reveal that the effectiveness of surfactants and denaturants to elute and denature adsorbed protein is significantly influenced by surface chemistry and the conditions from which the protein was adsorbed. These results provide a basis for the selection, design, and further development of chemical agents for protein elution and surface decontamination.