Compactness of the kinetic molten globule of bovine alpha-lactalbumin: a dynamic light scattering study

Conformational Transitions upon Maturation Rule Surface and pH-Responsiveness of α-Lactalbumin Microparticulates

De novo designed protein supramolecular structures are nowadays attracting much interest as highly performing biomaterials. While a clear advantage is provided by the intrinsic biocompatibility and biodegradability of protein and peptide building blocks, developing sustainable and green bottom up approaches for finely tuning the material properties still remains a challenge. Here, we present an experimental study on the formation of protein microparticles in the form of particulates from the protein α-lactalbumin using bulk mixing in water solution and high temperature. Once formed, the structure and stability of these spherical protein condensates change upon further thermal incubation while the size of aggregates does not significantly increase. Combining advanced microscopy and spectroscopy methods, we prove that this process, named maturation, is characterized by a gradual increase of amyloid-like structure in protein particulates, an enhancement in surface roughness and in molecular compactness, providing a higher stability and resistance of the structure in acidic environments. When dissolved at pH 2, early stage particulates disassemble into a homogeneous population of small oligomers, while the late stage particulates remain unaffected. Particulates at the intermediate stage of maturation partially disassemble into a heterogeneous population of fragments. Importantly, differently matured microparticles show different features when loading a model lipophilic molecule. Our findings suggest conformational transitions localized at the interface as a key step in the maturation of amyloid protein condensates, promoting this phenomenon as an intrinsic knob to tailor the properties of protein microparticles formed via bulk mixing in aqueous solution. This provides a simple and sustainable platform for the design and realization of protein microparticles for tailored applications.

Polymer Free Volume Effects on Protein Dynamics in Polystyrene Revealed by Single-Molecule Spectroscopy

Protein-polymer interactions are critical to applications ranging from biomedical devices to chromatographic separations. The mechanistic relationship between the microstructure of polymer chains and protein interactions is challenging to quantify and not well studied. Here, single-molecule microscopy is used to compare the dynamics of two model proteins, α-lactalbumin and lysozyme, at the interface of uncharged polystyrene with varied molecular weights. The two proteins exhibit different surface interaction mechanisms despite having a similar size and structure. α-Lactalbumin exhibits interfacial adsorption-desorption with residence times that depend on polymer molecular weight. Lysozyme undergoes a continuous time random walk at the polystyrene surface with residence times that also depend on the molecular weight of polystyrene. Single-molecule observables suggest that the hindered continuous time random walk dynamics displayed by lysozyme are determined by the polystyrene free volume, a finding supported by thermal annealing and solvent quality studies. Hindered dynamics are dominated by short-range hydrophobic interactions where the contributions of electrostatic forces are negligible. This work establishes a relationship between the microscale structure (i.e., free volume) of polystyrene polymer chains to nanoscale interfacial protein dynamics.

Structural and functional characterization of fast-cycling RhoF GTPase

Ras superfamily GTPases are molecular switches that cycle between GDP-bound inactive state and GTP-bound active state to control many signaling pathways. Emerging evidence suggests that several Ras superfamily GTPases, including RhoF, do not follow the classical GDP/GTP exchange cycle; they act as constitutively active GTP-bound proteins due to their fast activities of GDP/GTP exchange (termed as 'fast-cycling' GTPases). To understand the molecular basis of the fast-cycling GTPases, we generated a GTPase active recombinant RhoF and examined its function and structure. Two point mutations in the switch I/II regions (Q77L and P45S, corresponding to Q61L and P29S of Rac1) significantly reduced the GTPase activity of RhoF, suggesting a conserved mechanism of GTP hydrolysis between RhoF and other RAS superfamily GTPases. However, in contrary to the previous evidence, RhoF represented a slow GDP/GTP exchange activity that dissociates GDP very slowly on a day-to-week time scale, in our experiment using fluorescently labeled GDP. The slow GDP dissociation was accelerated by Mg²⁺ chelation and canonical fast-cycling mutations, F44L (corresponding to F28L of Rac1) and P45S. NMR and dynamic light scattering data revealed a multimeric structure of RhoF that can switch between different conformations depending on the GTP/GDP-bound state. Overall, our study suggests that (1) RhoF shares a conserved mechanism of GTP hydrolysis with other RAS superfamily GTPases, but (2) RhoF adopts a unique multimeric structure. Our study also argues that (3) the emerging concept of the fast-cycling GTPases for RhoF should be validated using an alternative assay that does not rely on fluorescently labeled GDP (251 words).

HSPB5 engages multiple states of a destabilized client to enhance chaperone activity in a stress-dependent manner

Small heat shock proteins (sHSPs) delay protein aggregation in an ATP-independent manner by interacting with client proteins that are in states susceptible to aggregation, including destabilized states related to cellular stress. Up-regulation of sHSPs under stress conditions supports their critical role in cellular viability. Widespread distribution of sHSPs in most organisms implies conservation of function, but it remains unclear whether sHSPs implement common or distinct mechanisms to delay protein aggregation. Comparisons among various studies are confounded by the use of different model client proteins, different assays for both aggregation and sHSP/client interactions, and variable experimental conditions used to mimic cellular stress. To further define sHSP/client interactions and their relevance to sHSP chaperone function, we implemented multiple strategies to characterize sHSP interactions with α-lactalbumin, a model client whose aggregation pathway is well defined. We compared the chaperone activity of human αB-crystallin (HSPB5) with HSPB5 variants that mimic states that arise under conditions of cellular stress or disease. The results show that these closely related sHSPs vary not only in their activity under identical conditions but also in their interactions with clients. Importantly, under nonstress conditions, WT HSPB5 delays client aggregation solely through transient interactions early in the aggregation pathway, whereas HSPB5 mutants that mimic stress-activated conditions can also intervene at later stages of the aggregation pathway to further delay client protein aggregation.

Spectroscopic and computational evaluation on the binding of safranal with human serum albumin: Role of inner filter effect in fluorescence spectral correction

For determining the pharmacological properties of medicinal compounds, their binding with serum albumins is very crucial. Herein, we have selected safranal, a major constituent of saffron which is known to retain a number of medicinal properties including antioxidant, anti-inflammatory, tumoricidal, anti-genotoxic, and anti-aging activities; and studied its mechanism of binding with human serum albumin at physiological pH using various spectroscopic methods along with computational approach using molecular docking. A change in the difference UV-visible spectrum of HSA in presence of safranal was found which is due to the complex formation. Owing to the strong absorption of safranal at the fluorescence excitation wavelength of HSA (295 nm) and in the whole range of emission, the fluorescence spectra of HSA in presence of safranal were corrected for the inner filter effect. After the correction the spectra were free from the safranal absorption effect and it was found that addition of safranal causes the quenching of HSA fluorescence and a blue shift of the emission maximum which are attributed to the binding of safranal to the protein and dominance of hydrophobic forces in the interaction, respectively. It was evident from the comparison of observed and corrected fluorescence spectra that before correction there was a large red shift while after correction appearance of blue shift was occurred. The involvement of hydrophobic interaction was also found from the extrinsic fluorescence measurements using ANS dye as well as from the analyzed thermodynamic parameters. Safranal was found to partially induce the secondary structure of HSA as construed from the CD measurements. The size of the HSA was also decreased as evident from the DLS and RLS measurements. Both site marker studies and molecular docking simulations suggested that the primary binding site of the safranal in the HSA is Sudlow's site 1 located in the subdomain IIA. Hydrophobic interaction provides the major contribution to the binding forces along with a little amount of hydrogen bonding.

Molecular mechanisms of the cytotoxicity of human α-lactalbumin made lethal to tumor cells (HAMLET) and other protein-oleic acid complexes

Although HAMLET (human α-lactalbumin made lethal to tumor cells), a complex formed by human α-lactalbumin and oleic acid, has a unique apoptotic activity for the selective killing of tumor cells, the molecular mechanisms of expression of the HAMLET activity are not well understood. Therefore, we studied the molecular properties of HAMLET and its goat counterpart, GAMLET (goat α-lactalbumin made lethal to tumor cells), by pulse field gradient NMR and 920-MHz two-dimensional NMR techniques. We also examined the expression of HAMLET-like activities of complexes between oleic acid and other proteins that form a stable molten globule state. We observed that both HAMLET and GAMLET at pH 7.5 were heterogeneous, composed of the native protein, the monomeric molten globule-like state, and the oligomeric species. At pH 2.0 and 50 °C, HAMLET and GAMLET appeared in the monomeric state, and we identified the oleic acid-binding site in the complexes by two-dimensional NMR. Rather surprisingly, the binding site thus identified was markedly different between HAMLET and GAMLET. Furthermore, canine milk lysozyme, apo-myoglobin, and β2-microglobulin all formed the HAMLET-like complex with the anti-tumor activity, when the protein was treated with oleic acid under conditions in which their molten globule states were stable. From these results, we conclude that the protein portion of HAMLET, GAMLET, and the other HAMLET-like protein-oleic acid complexes is not the origin of their cytotoxicity to tumor cells and that the protein portion of these complexes plays a role in the delivery of cytotoxic oleic acid molecules into tumor cells across the cell membrane.

A NAD(P) reductase like protein is the salicylic acid receptor in the appendix of the Sauromatum guttatum inflorescence

The mode of action of the thermogenic inducers (salicylic acid, aspirin, and 2,6-dihydroxybenzoic acid) in the appendix of the Sauromatum guttatum inflorescence is poorly understood. Using ESI-MS and light scattering analysis, we have demonstrated that NAD(P) reductase like protein (RL) is the salicylic acid receptor in the Sauromatum appendix. RL was self-assembled in water into a large unit with a hydrodynamic diameter of 800 nm. In the presence of 1 pM salicylic acid, RL exhibited discontinuous and reversible volume phase transitions. The volume phase changed from 800 to 300 nm diameter and vice versa. RL stayed at each volume phase for ~4-5 min with a fast relaxation time between the 2 phases. ESI-MS analysis of RL extracted from appendices treated with salicylic acid, aspirin, and 2,6-DHBA at a micromolar range demonstrated that these compounds are capable of inducing graded conformational changes that are concentration-dependent. A strong correlation between RL conformations and heat-production induced by salicylic acid was also observed. These preliminary findings reveal structural and conformational roles for RL by which plants regulate their temperature and synchronize their time keeping mechanisms.

Plasma protein adsorption to zwitterionic poly (carboxybetaine methacrylate) modified surfaces: chain chemistry and end-group effects on protein adsorption kinetics, adsorbed amounts and immunoblots

Protein-surface interactions are crucial to the overall biocompatability of biomaterials, and are thought to be the impetus towards the adverse host responses such as blood coagulation and complement activation. Only a few studies hint at the ultra-low fouling potential of zwitterionic poly(carboxybetaine methacrylate) (PCBMA) grafted surfaces and, of those, very few systematically investigate their non-fouling behavior. In this work, single protein adsorption studies as well as protein adsorption from complex solutions (i.e. human plasma) were used to evaluate the non-fouling potential of PCBMA grafted silica wafers prepared by nitroxide-mediated free radical polymerization. PCBMAs used for surface grafting varied in charge separating spacer groups that influence the overall surface charges, and chain end-groups that influence the overall hydrophilicity, thereby, allows a better understanding of these effects towards the protein adsorption for these materials. In situ ellipsometry was used to quantify the adsorbed layer thickness and adsorption kinetics for the adsorption of four proteins from single protein buffer solutions, viz, lysozyme, α-lactalbumin, human serum albumin and fibrinogen. Total amount of protein adsorbed on surfaces differed as a function of surface properties and protein characteristics. Finally, immunoblots results showed that human plasma protein adsorption to these surfaces resulted, primarily, in the adsorption of human serum albumin, with total protein adsorbed amounts being the lowest for PCBMA-3 (TEMPO). It was apparent that surface charge and chain hydrophilicity directly influenced protein adsorption behavior of PCBMA systems and are promising materials for biomedical applications.

Directing the oligomer size distribution of peroxidase-mediated cross-linked bovine alpha-lactalbumin

Enzymatic protein cross-linking is a powerful tool to change protein functionality. For optimal functionality in gel formation, the size of the cross-linked proteins needs to be controlled, prior to heating. In the current study, we addressed the optimization of the horseradish peroxidase-mediated cross-linking of calcium-depleted bovine alpha-lactalbumin. To characterize the formed products, the molecular weight distribution of the cross-linked protein was determined by size exclusion chromatography. At low ionic strength, more dimers of alpha-lactalbumin are formed than at high ionic strength, while the same conversion of monomers is observed. Similarly, at pH 5.9 more higher oligomers are formed than at pH 6.8. This is proposed to be caused by local changes in apo alpha-lactalbumin conformation as indicated by circular dichroism spectroscopy. A gradual supply of hydrogen peroxide improves the yield of cross-linked products and increases the proportion of higher oligomers. In conclusion, this study shows that the size distribution of peroxidase-mediated cross-linked alpha-lactalbumin can be directed toward the protein oligomers desired.

A magnetic microchip for controlled transport of attomole levels of proteins

A novel method of controlled transport of proteins immobilized on micrometre-sized magnetic beads in a lab-on-a-chip environment is presented. Bead motion is controlled by lithographically made magnetic elements forming transportation lines in combination with an applied in-plane rotating magnetic field. In this way, transport of attomole amounts of proteins is controlled with micrometre precision. Also, the activity of proteins immobilized on the beads is demonstrated by injecting antibodies into the system. A critical step in developing the method was to reduce sticking forces between beads and substrate during transportation of proteins. Charge interaction was found to be of minor importance compared to hydrophobic forces. To achieve a reliable transport of biologically active proteins, both substrate and beads were coated with polyethylene glycol (PEG) and the protein covered beads were suspended in buffer with surfactants. The described system fulfils all the important unit operations of a microfluidic platform and, as a further advantage, presents less need for microchannels and electric wiring.

Leishmania donovani trypanothione reductase: role of urea and guanidine hydrochloride in modulation of functional and structural properties

Trypanothione reductase [TR], an NADPH-dependent disulfide oxidoreductase, unique to kinetoplastid parasites including Trypanosoma and Leishmania, is a validated target for the design of improved drugs. TR is a stable homodimer with a FAD molecule tightly bound to each subunit. In this paper, structure, function, stability properties and cofactor protein interactions of recombinant TR from Leishmania donovani were investigated under equilibrium unfolding/denaturing conditions. Urea induced unfolding was non-reductive in nature and led to the formation of partially folded intermediate. This intermediate species lacks catalytic activity and characteristic conformation of native LdTR but has significant secondary structure and could be partially reactivated. Guanidine hydrochloride-induced irreversible denaturation was marked by the presence of molten globule intermediate. Reactivation and cross-linking experiments clearly demonstrated that the loss of activity at lower denaturant concentrations was not coincided by dimer dissociation or structural unfolding. The studies demonstrate that functional conformation and stability are largely governed by ionic interactions and active site disulfide plays a vital role in maintaining functional conformation. The results obtained from this study provide intriguing insight into the possible mechanism/s of modulation of structure, function and stability of LdTR induced by the cationic, guanidine hydrochloride and the neutral denaturant, urea.

Effect of alpha-lactalbumin on the phase behavior of AOT-brine-isooctane mixtures: role of charge interactions

We have found that both electrostatic and hydrophobic interactions are involved in the ability of the protein alpha-lactalbumin (alpha-LA) to affect the self-assembly of the anionic surfactant sodium bis(ethylhexyl) sulfosuccinate (AOT, 3.5 wt %) in equivolume mixtures of organic and aqueous solutions. The composition and size of AOT phase structures that form in the presence of 0.35 wt % protein were evaluated as a function of pH and ionic strength. In the absence of protein, AOT forms water-in-oil microemulsion droplets for all pH and salt concentrations studied here. The presence of the protein in the water-in-oil microemulsion phase boosts water solubilization and droplet size, as the spontaneous curvature of the surfactant interface becomes less negative. Aggregates of protein, surfactant, and oil also form in the water-continuous phase. The size and composition of structures in both phases can be tuned in the presence of protein by varying the pH and ionic strength. alpha-LA induces the appearance of an anisotropic surfactant phase at pH <5.8. At intermediate salt concentrations, a third isotropic, viscous aqueous phase appears that contains 55-60% of the protein, 10-14% of the surfactant, and significant amounts of oil. Circular dichroism and fluorescence spectroscopy indicate that the protein contains enhanced alpha-helical secondary structure when self-assembling with surfactant, and has a loosened tertiary structure. The protein does not interact with the surfactant as an unfolded random coil. Although the conformation of alpha-LA in aqueous salt solutions is known to depend on pH, when self-assembling with AOT the protein adopts a structure whose features are quite pH insensitive, and likely reflect an intrinsic interaction with the interface.

Matrix assisted refolding of proteins by ion exchange chromatography

Two different approaches of matrix assisted refolding have been evaluated and compared to conventional refolding by dilution. Bovine alpha-lactalbumin was used for the studies as model protein. It was adsorbed under denaturing conditions on an ion exchange matrix and refolding was completed on the column prior to elution or, depending on the buffer system, in the eluate. Agarose based chromatography matrices showed high capacities for the denatured alpha-lactalbumin. A positive effect on the yield of refolded protein by the matrix could be observed for Fractogel EMD DEAE and a negative for Toyopearl DEAE 650M, DEAE Sepharose FF and Q Sepharose FF. In the case of Fractogel EMD DEAE the ion exchange surface might act as a folding helper. This property may be caused by the grafted polymers. For Source 30Q only a marginal negative influence on the refolding kinetics was observed, thus the ion exchanger is only a mean for removal of chaotropic agents. Refolding on the column is characterized by a low yield but high productivity due to significant reduction of refolding time.

High-Throughput Screening of Protein Surface Activity via Flow Injection Analysis-pH Gradient-Dynamic Surface Tension Detection

Using flow injection analysis (FIA), a pH gradient is blended in real time with a protein sample as the pH-dependent protein surface activity is measured by a dynamic surface tension detector (FIA-pH-DSTD). This instrumental system was developed as a high-throughput method for the screening of protein surface activity at the air/liquid interface as a function of pH. This method utilizes the continuous flow, drop-based dynamic surface tension detector in combination with flow injection sample introduction and blending of a steady-state concentration of protein sample with a pH gradient ranging from pH 2.0 to pH 11.5. Dynamic surface tension is measured through the differential pressure across the air/liquid interface of repeatedly growing and detaching drops. Continuous surface tension measurement is achieved for each eluting drop of 2-s length (2 muL), providing insight into both the kinetic and thermodynamic behaviors of molecular orientation processes at the liquid/air interface. Three-dimensional data are obtained, with surface tension first converted to surface pressure, which is collected as a function of elution time versus drop time. In FIA-pH-DSTD, a commercial pH probe is used to measure pH during elution time, enabling surface pressure throughout drop time to be subsequently plotted as a function of eluting pH. An automated DSTD calibration procedure and data analysis method is applied, which allows simultaneous use of two different solvents, permitting real-time dynamic surface tension data to be obtained. The method was applied to the analysis of 14 commercial purified proteins, yielding characteristic features of surface activity as a function of pH. The reproducibility of the measurement and selectivity advantage of the DSTD was shown for the analysis of serum albumins from various mammalian sources. Several applications were also suggested and discussed in order to show the potential of the method for protein and food chemistry studies and in the study of protein-polymer interactions.

Increasing Stability Reduces Conformational Heterogeneity in a Protein Folding Intermediate Ensemble

A multi-site, time-resolved fluorescence resonance energy transfer methodology has been used to study structural heterogeneity in a late folding intermediate ensemble, IL, of the small protein barstar. Four different intra-molecular distances have been measured within the structural components of IL. The IL ensemble is shown to consist of different sub-populations of molecules, in each of which one or more of the four distances are native-like and the remaining distances are unfolded-like. In very stable conditions that favor formation of IL, all four distances are native-like in most molecules. In less stable conditions, one or more distances are unfolded-like. As stability is decreased, the proportion of molecules with unfolded-like distances increases. Thus, the results show that protein folding intermediates are ensembles of different structural forms, and they demonstrate that conformational entropy increases as structures become less stable. These observations provide direct experimental evidence in support of a basic tenet of energy landscape theory for protein folding, that available conformational space, as represented by structural heterogeneity in IL, becomes restricted as the stability is increased. The results also vindicate an important prediction of energy landscape theory, that different folding pathways may become dominant under different folding conditions. In more stable folding conditions, uniformly native-like compactness is achieved during folding to IL, whereas in less stable conditions, uniformly native-like compactness is achieved only later during the folding of IL to N.

Photon correlation spectroscopy investigations of proteins

Physical principles of photon correlation spectroscopy (PCS), mathematical treatment of the PCS data (converting autocorrelation functions to distribution functions or average characteristics), and PCS applications to study proteins and other biomacromolecules in aqueous media are described and analysed. The PCS investigations of conformational changes in protein molecules, their aggregation itself or in consequence of interaction with other molecules or organic (polymers) and inorganic (e.g. fumed silica) fine particles as well as the influence of low molecular compounds (surfactants, drugs, salts, metal ions, etc.) reveal unique capability of the PCS techniques for elucidation of important native functions of proteins and other biomacromolecules (DNA, RNA, etc.) or microorganisms (Escherichia coli, Pseudomonas putida, Dunaliella viridis, etc.). Special attention is paid to the interaction of proteins with fumed oxides and the impact of polymers and fine oxide particles on the motion of living flagellar microorganisms analysed by means of PCS.

Effect of added α-lactalbumin protein on the phase behavior of AOT–brine–isooctane systems

We have found that the presence of <1 wt% of the globular protein alpha-lactalbumin has a significant impact on the equilibrium phase behavior of dilute sodium bis(ethylhexyl) sulfosuccinate (AOT)/brine/isooctane systems. Nuclear magnetic resonance (NMR), Karl Fischer titration, and ultraviolet spectroscopy were used to determine the surfactant, oil, water, and protein content of the organic and aqueous phases as a function of the total surfactant and protein present. As a small amount of alpha-lactalbumin is added to the mixture, there is a substantial increase (up to 80%) in the maximum water solubility in the water-in-oil microemulsion phase. Dynamic light scattering measurements indicate that this increase is due to a decrease in the magnitude of the (negative) spontaneous curvature of the surfactant monolayer, as droplets swell in size. As the molar ratio of alpha-lactalbumin to AOT surpasses approximately 1:300, the partitioning of water, protein, and surfactant shifts to the excess aqueous phase, where soluble assemblies with positive curvature are detected by dynamic light scattering. Significant amounts of isooctane are solubilized in these aggregates, consistent with the formation of oil-in-water microemulsion droplets. Circular dichroism studies showed that the tertiary structure of the protein in the microemulsion is disrupted while the secondary structure is increased. In light of these findings, the protein most likely expands to a molten-globule type conformation in the AOT interfacial environment, but does not substantially unfold to become an extended chain.

Equilibrium and kinetic folding of hen egg-white lysozyme under acidic conditions

The equilibrium and kinetic folding of hen egg-white lysozyme was studied by means of circular dichroism spectra in the far- and near-ultraviolet (UV) regions at 25 degrees C under the acidic pH conditions. In equilibrium condition at pH 2.2, hen lysozyme shows a single cooperative transition in the GdnCl-induced unfolding experiment. However, in the GdnCl-induced unfolding process at lower pH 0.9, a distinct intermediate state with molten globule characteristics was observed. The time-dependent unfolding and refolding of the protein were induced by concentration jumps of the denaturant and measured by using stopped-flow circular dichroism at pH 2.2. Immediately after the dilution of denaturant, the kinetics of refolding shows evidence of a major unresolved far-UV CD change during the dead time (<10 ms) of the stopped-flow experiment (burst phase). The observed refolding and unfolding curves were both fitted well to a single-exponential function, and the rate constants obtained in the far- and near-UV regions coincided with each other. The dependence on denaturant concentration of amplitudes of burst phase and both rate constants was modeled quantitatively by a sequential three-state mechanism, U<-->I<-->N, in which the burst-phase intermediate (I) in rapid equilibrium with the unfolded state (U) precedes the rate-determining formation of the native state (N). The role of folding intermediate state of hen lysozyme was discussed.

Molten globule of bovine alpha-lactalbumin at neutral pH induced by heat, trifluoroethanol, and oleic acid: a comparative analysis by circular dichroism spectroscopy and limited proteolysis

The calcium-depleted form of alpha-lactalbumin (alpha-LA) at neutral pH can be induced to adopt a partly folded state or molten globule upon moderate heating, by dissolving the protein in aqueous TFE or by adding oleic acid. This last folding variant of the protein, named HAMLET, can induce apoptosis in tumor cells. The aim of the present work was to unravel from circular dichroism (CD) measurements and proteolysis experiments structural features of the molten globule of apo-alpha-LA at neutral pH. CD spectra revealed that the molten globule of apo-alpha-LA can be obtained upon mild heating at 45 degrees C, as well as at room temperature in the presence of 15% TFE or by adding to the protein solution 7.5 equivalents of oleic acid. Under these various conditions the far- and near-UV CD spectra of apo-alpha-LA are essentially identical to those of the most studied molten globule of alpha-LA at pH 2.0 (A-state). Proteolysis of the 123-residue chain of apo-alpha-LA by proteinase K at 4 degrees C occurs slowly as an all-or-none process leading to small peptides only. At 37 degrees C, proteinase K preferentially cleaves apo-alpha-LA at peptide bonds Ser34-Gly35, Gln39-Ala40, Gln43-Asn44, Phe53-Gln54, and Asn56-Asn57. All these peptide bonds are located at level of the beta-subdomain of the protein (chain region 34-57). Similar sites of preferential cleavage have been observed with the TFE- and oleic acid-induced molten globule of apo-alpha-LA. A protein species given by the N-terminal fragment 1-34 linked via the four disulfide bridges to the C-terminal fragment 54-123 or 57-123 can be isolated from the proteolytic mixture. The results of this study indicate that the same molten globule state of apo-alpha-LA can be obtained at neutral pH under mildly denaturing conditions, as indicated by using a classical spectroscopic technique such as CD and a simple biochemical approach as limited proteolysis. We conclude that the molten globule of alpha-LA maintains a native-like tertiary fold characterized by a rather well-structured alpha-domain and a disordered chain region encompassing the beta-subdomain 34-57 of the protein.

Intradomain disulfide bonds impede formation of the alternatively folded state of antibody chains

Antibodies undergo significant conformational changes upon acidification, leading to the formation of an alternatively folded state. Here, we analyzed the conformation of MAK 33 Fab and its light chain at acidic pH, both in the reduced and oxidized form. At acidic pH, the proteins exhibited a highly structured, but non-native conformation, corresponding to the alternatively folded state, previously described for the intact antibody. However, the requirements to form this alternative structure were different for the oxidized and reduced protein. Whereas in the oxidized form of the immunoglobulin light chain the alternatively folded state could only be detected at pH<1.4, the reduced light chain already adopted this structure at pH 2. Thermal denaturation measurements revealed that, surprisingly, the alternatively folded state of the reduced light chain was more stable than that of the oxidized protein at pH 1.4. This indicates that the intradomain disulfide bonds, which stabilize the native state of antibody domains, impede the formation of the alternatively folded state.

Acid and Chemical Induced Conformational Changes of Ervatamin B. Presence of Partially Structured Multiple Intermediates

The structural and functional aspects of ervatamin B were studied in solution. Ervatamin B belongs to the alpha + beta class of proteins. The intrinsic fluorescence emission maximum of the enzyme was at 350 nm under neutral conditions, and at 355 nm under denaturing conditions. Between pH 1.0- 2.5 the enzyme exists in a partially unfolded state with minimum or no tertiary structure, and no proteolytic activity. At still lower pH, the enzyme regains substantial secondary structure, which is predominantly a beta-sheet conformation and shows a strong binding to 8-anilino-1- napthalene-sulfonic acid (ANS). In the presence of salt, the enzyme attains a similar state directly from the native state. Under neutral conditions, the enzyme was stable in urea, while the guanidine hydrochloride (GuHCl) induced equilibrium unfolding was cooperative. The GuHCl induced unfolding transition curves at pH 3.0 and 4.0 were non-coincidental, indicating the presence of intermediates in the unfolding pathway. This was substantiated by strong ANS binding that was observed at low concentrations of GuHCl at both pH 3.0 and 4.0. The urea induced transition curves at pH 3.0 were, however, coincidental, but non-cooperative. This indicates that the different structural units of the enzyme unfold in steps through intermediates. This observation is further supported by two emission maxima in ANS binding assay during urea denaturation. Hence, denaturant induced equilibrium unfolding pathway of ervatamin B, which differs from the acid induced unfolding pathway, is not a simple two-state transition but involves intermediates which probably accumulate at different stages of protein folding and hence adds a new dimension to the unfolding pathway of plant proteases of the papain superfamily.

Stepwise proteolytic removal of the beta subdomain in alpha-lactalbumin. The protein remains folded and can form the molten globule in acid solution

Bovine alpha-lactalbumin (alpha-LA) is an alpha/beta protein which adopts partly folded states when dissolved at low pH (A-state), by removal of the protein-bound calcium at neutral pH and low salt concentration (apo-state), as well as in aqueous trifluoroethanol. Previous spectroscopic studies have indicated that the A-state of alpha-LA at pH 2.0, considered a prototype molten globule, has a native-like fold in which the helical core is mostly retained, while the beta subdomain is less structured. Here, we investigate the conformational features of three derivatives of alpha-LA characterized by a single peptide bond fission or a deletion of 12 or 19/22 amino-acid residues of the beta subdomain of the native protein (approximately from residue 34 to 57). These alpha-LA derivatives were obtained by limited proteolysis of the protein in its partly folded state(s). A nicked alpha-LA species consisting of fragments 1-,3-40 and 41-123 (nicked-LA) was prepared by thermolytic digestion of the 123-residue chain of alpha-LA in 50% (v/v) aqueous trifluoroethanol. Two truncated or gapped protein species given by fragments 1-40 and 53-123 (desbeta1-LA) or fragments 1-34 and 54-,57-123 (desbeta2-LA) were obtained by digestion of alpha-LA with pepsin in acid or with proteinase K at neutral pH in its apo-state, respectively. The two protein fragments of nicked or gapped alpha-LA are covalently linked by the four disulfide bridges of the native protein. CD measurements revealed that, in aqueous solution at neutral pH and in the presence of calcium, the three protein species maintain the helical secondary structure of intact alpha-LA, while the tertiary structure is strongly affected by the proteolytic cleavages of the chain. Temperature effects of CD signals in the far- and near-UV region reveal a much more labile tertiary structure in the alpha-LA derivatives, while the secondary structure is mostly retained even upon heating. In acid solution at pH 2.0, the three alpha-LA variants adopt a conformational state essentially identical to the molten globule displayed by intact alpha-LA, as demonstrated by CD measurements. Moreover, they bind strongly the fluorescent dye 8-anilinonaphthalene-1-sulfonate, which is considered a diagnostic feature of the molten globule of proteins. Therefore, the beta subdomain can be removed from the alpha-LA molecule without impairing the capability of the rest of the chain to adopt a molten globule state. The results of this protein dissection study provide direct experimental evidence that in the alpha-LA molten globule only the alpha domain is structured.

The structure of denatured alpha-lactalbumin elucidated by the technique of disulfide scrambling: fractionation of conformational isomers of alpha-lactalbumin

The structure of denatured alpha-lactalbumin (alpha-LA) has been characterized using the method of disulfide scrambling. Under denaturing conditions (urea, guanidine hydrochloride, guanidine thiocyanate, organic solvent or elevated temperature) and in the presence of thiol initiator, alpha-LA denatures by shuffling its four native disulfide bonds and converts to a mixture of fully oxidized scrambled structures. Analysis by reversed-phase HPLC reveals that the denatured alpha-LA comprises a minimum of 45 fractions of scrambled isomers. Among them, six well populated isomers have been isolated and structurally characterized. Their relative concentrations, which represent the fingerprinting of the denatured alpha-LA, vary substantially under different denaturing conditions. These results permit independent plotting of the denaturation and unfolding curves of alpha-LA. Most importantly, unique isomers of partially unfolded alpha-LA were shown to populate at mild and selected denaturing conditions. Organic solvent disrupts preferentially the hydrophobic alpha-helical domain, generating a predominant isomer containing two native disulfide bonds at the beta-sheet domain and two scrambled disulfide bonds at the alpha-helical region. Thermal denaturation selectively unfolds the beta-sheet domain of alpha-LA, producing a prevalent isomer that exhibits structural characteristics of the molten globule state of alpha-LA.

The Effect of Solute Concentration on Equilibrium Partitioning in Polymeric Gels

The effect of solute concentration on the equilibrium partitioning of sphere-like, colloidal solutes in stiff polymer hydrogels is examined theoretically and experimentally. The theoretical development is a statistical mechanics approach, and allows quantitative calculations to be performed to determine the concentration-dependent partition coefficient correct to first order in solute concentration at specific surface charge densities. The theory predicts that repulsive steric and/or electrostatic solute-fiber interactions exclude solute from the gel phase, but that repulsive solute-solute interactions cause partitioning into the gel to increase with increasing solute concentration. These trends are enhanced for larger solutes, increased fiber volume fractions, or stronger electrostatic repulsion. Partition coefficients have also been measured for two proteins, bovine serum albumin (BSA) and alpha-lactalbumin (ALA), in a system consisting of a salt solution and cubes of agarose hydrogel. To investigate the effect of electrostatic interactions, the experiments were performed at 0.15 M KCl and 0.01 M KCl. The theory underpredicts the strong electrostatic repulsion between BSA macromolecules at the lower ionic strength. The experimental results for ALA show the influence of an attractive interaction between the protein macromolecules, in addition to hard-sphere repulsive and electrostatic interactions. Copyright 2001 Academic Press.

Folding pathway mediated by an intramolecular chaperone: the structural and functional characterization of the aqualysin I propeptide

Aqualysin I, a thermostable homologue of subtilisin, requires its propeptide (ProA) to function as an intramolecular chaperone (IMC). To decipher the mechanisms through which propeptides can initiate protein folding, we characterized ProA in terms of its sequence, structure and function. Our results show that, in contrast to ProS (propeptide of subtilisin), ProA can fold spontaneously, reversibly and cooperatively into a stable monomeric alpha-beta conformation, even when isolated from its cognate protease-domain. ProA displays an indiscernible amount of tertiary structure with a considerable solvent-accessible hydrophobic surface, but is not a classical molten-globule folding intermediate. Moreover, despite showing only 21 % sequence identity with ProS, ProA can not only inhibit enzymatic activity with a magnitude tenfold greater than ProS, but can also chaperone subtilisin folding, albeit with a lower efficiency. The structure of ProA complexed with subtilisin is different from that of isolated ProA. Hence, additional interactions seem necessary to induce ProA into a compact structure. Our results also suggest that: (a) propeptides that are potent inhibitors are not necessarily better IMCs; (b) propeptides within the subtilase family appear polymorphic and; (c) the intrinsic instability within propeptides may be necessary for rapid activation of the cognate protein.

A stabilized molten globule protein

A predominant conformational isomer of non-native alpha-lactalbumin (alpha-LA) has been purified by thermal denaturation of the native alpha-LA using the technique of disulfide scrambling. This unique isomer retains a substantial content of alpha-helical structure. It is stabilized by two native disulfide bonds within the alpha-helical domain and two scrambled non-native disulfide bonds at the beta-sheet domain. This denatured isomer of alpha-LA exhibits structural characteristics that are consistent with the well-documented molten globule state. The ability to prepare a stabilized and structurally defined molten globule provides a useful model for studying the folding and unfolding pathways of proteins.

The slow folding reaction of barstar: the core tryptophan region attains tight packing before substantial secondary and tertiary structure formation and final compaction of the polypeptide chain

The slow folding of a single tryptophan-containing mutant of barstar has been studied in the presence of 2 M urea at 10 degrees C, using steady state and time-resolved fluorescence methods and far and near-UV CD measurements. The protein folds in two major phases: a fast phase, which is lost in the dead time of measurement during which the polypeptide collapses to a compact form, is followed by a slow observable phase. During the fast phase, the rotational correlation time of Trp53 increases from 2.2 ns to 7.2 ns, and its mean fluorescence lifetime increases from 2.3 ns to 3.4 ns. The fractional changes in steady-state fluorescence, far-UV CD, and near-UV CD signals, which are associated with the fast phase are, respectively, 36 %, 46 %, and 16 %. The product of the fast phase can bind the hydrophobic dye ANS. These observations together suggest that the folding intermediate accumulated at the end of the fast phase has: (a) about 20 % of the native-state secondary structure, (b) marginally formed or disordered tertiary structure, (c) a water-intruded and mobile protein interior; and (d) solvent-accessible patches of hydrophobic groups. Measurements of the anisotropy decay of Trp53 suggest that it undergoes two types of rotational motion in the intermediate: (i) fast (tau(r) approximately 1 ns) local motion of its indole side-chain, and (ii) a slower (tau(r) approximately 7.2 ns) motion corresponding to global tumbling of the entire protein molecule. The ability of the Trp53 side-chain to undergo fast local motion in the intermediate, but not in the fully folded protein where it is completely buried in the hydrophobic core, suggests that the core of the intermediate is still poorly packed. The global tumbling time of the fully folded protein is faster at 5.6 ns, suggesting that the volume of the intermediate is 25 % more than that of the fully folded protein. The rate of folding of this intermediate to the native state, measured by steady-state fluorescence, far-UV CD, and near-UV CD, is 0.07(+/-0.01) min(-1) This rate compares to a rate of folding of 0.03(+/-0.005) min(-1), determined by double-jump experiments which monitor directly formation of native protein; and to a rate of folding of 0.05 min(-1), when determined from time-resolved anisotropy measurements of the long rotational correlation time, which relaxes from an initial value of 7.2 ns to a final value of 5. 6 ns as the protein folds. On the other hand, the amplitude of the short correlation time decreases rapidly with a rate of 0.24(+/-0.06) min(-1). These results suggest that tight packing of residues in the hydrophobic core occurs relatively early during the observable slow folding reaction, before substantial secondary and tertiary structure formation and before final compaction of the protein.

A view of dynamics changes in the molten globule-native folding step by quasielastic neutron scattering

In order to understand the changes in protein dynamics that occur in the final stages of protein folding, we have used neutron scattering to probe the differences between a protein in its folded state and the molten globule states. The internal dynamics of bovine alpha-lactalbumin (BLA) and its molten globules (MBLA) have been examined using incoherent, quasielastic neutron scattering (IQNS). The IQNS results show length scale dependent, pico-second dynamics changes on length scales from 3.3 to 60 A studied. On shorter-length scales, the non-exchangeable protons undergo jump motions over potential barriers, as those involved in side-chain rotamer changes. The mean potential barrier to local jump motions is higher in BLA than in MBLA, as might be expected. On longer length scales, the protons undergo spatially restricted diffusive motions with the diffusive motions being more restricted in BLA than in MBLA. Both BLA and MBLA have similar mean square amplitudes of high frequency motions comparable to the chemical bond vibrational motions. Bond vibrational motions thus do not change significantly upon folding. Interestingly, the quasielastic scattering intensities show pronounced maxima for both BLA and MBLA, suggesting that "clusters" of atoms are moving collectively within the proteins on picosecond time scales. The correlation length, or "the cluster size", of such atom clusters moving collectively is dramatically reduced in the molten globules with the correlation length being 6.9 A in MBLA shorter than that of 18 A in BLA. Such collective motions may be important for the stability of the folded state, and may influence the protein folding pathways from the molten globules.

Limited proteolysis of bovine alpha-lactalbumin: isolation and characterization of protein domains

The partly folded states of alpha-lactalbumin (alpha-LA) exposed to acid solution at pH 2.0 (A-state) or at neutral pH upon EDTA-mediated removal of the single protein-bound calcium ion (apo form) have been probed by limited proteolysis experiments. These states are nowadays commonly considered to be molten globules and thus protein-folding intermediates. Pepsin was used for proteolysis at acid pH, while proteinase K and chymotrypsin at neutral pH. The expectations were that these proteolytic probes would detect sites and/or chain regions in the partly folded states of alpha-LA sufficiently dynamic, or even unfolded, capable of binding and adaptation to the specific stereochemistry of the protease's active site. A time-course analysis of the proteolytic events revealed that the fast, initial proteolytic cuts of the 123-residue chain of alpha-LA in its A-state or apo form by the three proteases occur at the same chain region 39-54, the actual site(s) of cleavage depending upon the protease employed. This region in native alpha-LA encompasses the beta-sheets of the protein. Subsequent cleavages occur mostly at chain regions 31-35 and 95-105. Four fragment species of alpha-LA have been isolated by reverse-phase high-performance liquid chromatography, and their conformational properties examined by circular dichroism and fluorescence emission spectroscopy. The single chain fragment 53-103, containing all the binding sites for calcium in native alpha-LA and cross-linked by two disulfide bridges, maintains in aqueous buffer and in the presence of calcium ions a folded structure characterized by the same content of alpha-helix of the corresponding chain segment in native alpha-LA. Evidence for some structure was also obtained for the two-chain species 1-40 and 104-123, as well as 1-31 and 105-123, both systems being covalently linked by two disulfide bonds. In contrast, the protein species given by fragment 1-34 connected to fragment 54-123 or 57-123 via four disulfide bridges adopts in solution a folded structure with the helical content expected for a native-like conformation. Of interest, the proteolytic fragment species herewith isolated correspond to the structural domains and subdomains of alpha-LA that can be identified by computational analysis of the three-dimensional structure of native alpha-LA (Siddiqui AS, Barton GI, 1995, Protein Sci 4:872-884). The fast, initial cleavages at the level of the beta-sheet region of native alpha-LA indicate that this region is highly mobile or even unfolded in the alpha-LA molten globule(s), while the rest of the protein chain maintains sufficient structure and rigidity to prevent extensive proteolysis. The subsequent cleavages at chain segment 95-105 indicate that also this region is somewhat mobile in the A-state or apo form of the protein. It is concluded that the overall domain topology of native alpha-LA is maintained in acid or at neutral pH upon calcium depletion. Moreover, the molecular properties of the partly folded states of alpha-LA deduced here from proteolysis experiments do correlate with those derived from previous NMR and other physicochemical measurements.

Kinetic and equilibrium intermediate states are different in LYLA1, a chimera of lysozyme and alpha-lactalbumin

For several proteins, a striking resemblance has been observed between the equilibrium partially folded state and the kinetic burst-phase intermediate, observed just after the dead-time in refolding experiments. This has led to the general statement that the conformation of both types of intermediates is similar. We show, at least for one of the proteins investigated here, that, although both states have some common characteristics, they are not identical. LYLA1 is a chimeric protein resulting from the transplantation of the Ca(2+)-binding loop and the adjacent helix C of bovine alpha-lactalbumin into the homologous position (residues 76-102) in human lysozyme. The apo-form of LYLA1 unfolds through a partially folded state, in analogy with the folding behaviour of the structurally homologous alpha-lactalbumin. The folding kinetics of LYLA1 and of its wild-type homologue, human lysozyme, are investigated by means of stopped-flow fluorescence and CD spectroscopy. In the case of human lysozyme, refolding involves parallel pathways as indicated by experiments in the presence of a fluorescent inhibitor. For apo-LYLA1, the burst-phase intermediate is compared with the equilibrium intermediate. At neutral pH, both states correspond, in that an important amount of secondary structure has been established, but the burst-phase intermediate is shown to be significantly less stable than the equilibrium intermediate. At pH 1.85, in the presence of 1.5 M guanidinium hydrochloride (GdnHCl) and at 25 degrees C, the equilibrium partially folded state of LYLA1 is 100% populated. When LYLA1 is rapidly diluted from 6 M GdnHCl to 1.5 M under these conditions, a time-dependent evolution of the fluorescence signal is observed, reflecting the transition from a burst-phase to a different equilibrium intermediate. These results provide strong evidence for the non-identity of both states in this protein.

Trifluoroethanol-induced conformational transitions of proteins: insights gained from the differences between alpha-lactalbumin and ribonuclease A

The trifluoroethanol (TFE)-induced structural changes of two proteins widely used in folding experiments, bovine alpha-lactalbumin, and bovine pancreatic ribonuclease A, have been investigated. The experiments were performed using circular dichroism spectroscopy in the far- and near-UV region to monitor changes in the secondary and tertiary structures, respectively, and dynamic light scattering to measure the hydrodynamic dimensions and the intermolecular interactions of the proteins in different conformational states. Both proteins behave rather differently under the influence of TFE: alpha-lactalbumin exhibits a molten globule state at low TFE concentrations before it reaches the so-called TFE state, whereas ribonuclease A is directly transformed into the TFE state at TFE concentrations above 40% (v/v). The properties of the TFE-induced states are compared with those of equilibrium and kinetic intermediate states known from previous work to rationalize the use of TFE in yielding information about the folding of proteins. Additionally, we report on the properties of TFE/water and TFE/buffer mixtures derived from dynamic light scattering investigations under conditions used in our experiments.