Extrinsic fluorescent dyes as tools for protein characterization

Histidine-tag-directed chromophores for tracer analyses in the analytical ultracentrifuge

Many recombinant proteins carry an oligohistidine (His(X))-tag that allows their purification by immobilized metal affinity chromatography (IMAC). This tag can be exploited for the site-specific attachment of chromophores and fluorophores, using the same metal ion-nitrilotriacetic acid (NTA) coordination chemistry that forms the basis of popular versions of IMAC. Labeling proteins in this way can allow their detection at wavelengths outside of the absorption envelopes of un-modified proteins and nucleic acids. Here we describe use of this technology in tracer sedimentation experiments that can be performed in a standard analytical ultracentrifuge equipped with absorbance or fluorescence optics. Examples include sedimentation velocity in the presence of low molecular weight chromophoric solutes, sedimentation equilibrium in the presence of high concentrations of background protein and selective labeling to simplify the assignment of species in a complex interacting mixture.

Quantitation, visualization, and monitoring of conformational transitions of human serum albumin by a tetraphenylethene derivative with aggregation-induced emission characteristics

Human serum albumin (HSA) is a major protein component of blood plasma, and its assay is of obvious value to biological research. We, herein, present a readily accessible fluorescent bioprobe for HSA detection and quantitation. A nonemissive tetraphenylethene derivative named sodium 1,2-bis[4-(3-sulfonatopropoxyl)phenyl]-1,2-diphenylethene (BSPOTPE) is induced to emit by HSA, showing a novel phenomenon of aggregation-induced emission (AIE). The AIE bioprobe enjoys a broad working range (0-100 nM), a low detection limit (down to 1 nM), and a superior selectivity to albumins. The fluorescent bioassay is unperturbed by the miscellaneous bioelectrolytes in the artificial urine. The AIE luminogen can also be used as a rapid and sensitive protein stain in gel electrophoresis for HSA visualization. Utilizing the AIE feature of BSPOTPE and the Forster resonance energy transfer from HSA to BSPOTPE, the unfolding process of HSA induced by guanidine hydrochloride is monitored, which reveals a multistep transition with the involvement of molten globule intermediates. Computational modeling suggests that the AIE luminogens dock in the hydrophobic cleft between subdomains IIA and IIIA of HSA with the aid of hydrophobic effect, charge neutralization, and hydrogen bonding interactions, offering mechanistic insight into the microenvironment inside the hydrophobic cavity.

The use of flow cytometry for the detection of subvisible particles in therapeutic protein formulations

The amount, identity, and size distribution of particles in parenteral therapeutic protein formulations are of immense interest due to potential safety and efficacy-related implications. In this communication, we describe the use of a flow cytometer equipped with forward- and side-scattering as well as fluorescence detectors, to determine the number of subvisible particles in monoclonal antibody formulations. The method appears to detect particles of size 1 μ and larger, requiring relatively small sample volumes to estimate subvisible particle counts. Additionally, it facilitates differentiation of proteinaceous particles after staining with a fluorescent hydrophobic dye. The method is expected to be particularly well suited for pharmaceutical development, because it provides increased throughput due to the use of a 96-well autosampler.

Thermodynamic analysis of ligand-induced changes in protein thermal unfolding applied to high-throughput determination of ligand affinities with extrinsic fluorescent dyes

The quantification of protein-ligand interactions is essential for systems biology, drug discovery, and bioengineering. Ligand-induced changes in protein thermal stability provide a general, quantifiable signature of binding and may be monitored with dyes such as Sypro Orange (SO), which increase their fluorescence emission intensities upon interaction with the unfolded protein. This method is an experimentally straightforward, economical, and high-throughput approach for observing thermal melts using commonly available real-time polymerase chain reaction instrumentation. However, quantitative analysis requires careful consideration of the dye-mediated reporting mechanism and the underlying thermodynamic model. We determine affinity constants by analysis of ligand-mediated shifts in melting-temperature midpoint values. Ligand affinity is determined in a ligand titration series from shifts in free energies of stability at a common reference temperature. Thermodynamic parameters are obtained by fitting the inverse first derivative of the experimental signal reporting on thermal denaturation with equations that incorporate linear or nonlinear baseline models. We apply these methods to fit protein melts monitored with SO that exhibit prominent nonlinear post-transition baselines. SO can perturb the equilibria on which it is reporting. We analyze cases in which the ligand binds to both the native and denatured state or to the native state only and cases in which protein:ligand stoichiometry needs to treated explicitly.

Encapsulation of anilinonaphthalenesulfonates in carboxylate-terminated PAMAM dendrimer at the polarized water|1,2-dichloroethane interface

Molecular encapsulation of water-soluble anionic fluorescent dye molecules, 8-anilino-1-naphthalenesulfonic acid (ANS), and its bimolecular derivative (bis-ANS), in the generation 3.5 polyamidoamine (G3.5 PAMAM) dendrimer was investigated in the bulk aqueous phase and at the polarized water|1,2-dichloroethane interface. ANS(-) was electrostatically incorporated in the dendrimer, and the fluorescence enhancement with a blue shift of the emission maximum was observed at pH values <6, where the interior of the dendrimer was positively charged. The fluorescence enhancement of ANS was maximized around pH 3 and then decreased under more acidic conditions. The potential dependences of the molecular encapsulation and the interfacial mechanism were studied in detail by means of potential modulated fluorescence (PMF) spectroscopy. Under acidic conditions, the dendrimer incorporated ANS(-) at the positively polarized interface as well as in the aqueous phase. ANS(-) was released from the dendrimer at the intrinsic transfer potential and independently transferred across the interface. Bis-ANS exhibited relatively strong interaction with the dendrimer over a wide pH range (1 < pH < 8), and a negative shift of the transfer potential was observed under the corresponding pH condition. The PMF analysis clearly demonstrated that the interfacial mechanism of the dendrimer involves transfer and adsorption processes depending on the pH condition and the Galvani potential difference.

Identifying the bond responsible for the fluorescence modulation in an amyloid fibril sensor

An ultrafast intramolecular bond twisting process is known to be the responsible mechanism for the sensing activity of the extensively used amyloid fibril sensor thioflavin T (ThT). However, it is not yet known which one of the two possible single bonds in ThT is actually involved in the twisting process. To resolve this fundamental issue, two derivatives of ThT have been designed and synthesized and subsequently their photophysical properties have been studied in different solvents. It is understood from the present study that the rotation around the central C-C single bond, and not that around the C-N single bond, is primarily responsible for the sensor activity of ThT. Detailed viscosity-dependent fluorescence studies revealed that the ThT derivative with restricted C-N bond rotation acts as a better sensor than the derivative with free C-N bond rotation. The better sensory activity is directly correlated with a shorter excited-state lifetime. Results obtained from the photophysical studies of the ThT derivatives have also been supported by the results obtained from quantum chemical calculations.

An oligomeric equilibrium intermediate as the precursory nucleus of globular and fibrillar supramacromolecular assemblies in a PDZ domain

The equilibrium unfolding at neutral pH of the third PDZ domain of PSD95, as followed by DSC, is characterized by the presence of an equilibrium intermediate with clear signs of oligomerization. DLS and SEC measurements indicate that at 60-70 degrees C small oligomers populate, showing a typical beta-sheet far-UV CD spectrum. These intermediate species lead to the formation of rodlike particulates of approximately 12 nm, which remain in solution after 2 weeks incubation and grow until they adopt annular/spherical shapes of approximately 50 nm and protofibrils, which are subsequently fully transformed into fibrils. The fibrils can also disaggregate after the addition of 1:1 buffer dilution followed by cooling to room temperature, thus returning to the initial monomeric state. Growth kinetics, as shown by ThT and ANS fluorescence, show that the organization of the different supramacromolecular structures comes from a common nucleation unit, the small oligomers, which organize themselves before reaching the incubation temperature of 60 degrees C. Our experiments point toward the existence of a well-defined reversible, stepwise, and downhill organization of the processes involved in the association-dissociation of the intermediate. We estimate the enthalpy change accompanying the association-dissociation equilibria to be 130 kJ x mol(-1). Furthermore, the coalescence under essentially reversible conditions of different kinds of supramacromolecular assemblies renders this protein system highly interesting for biophysical studies aimed at our further understanding of amyloid pathological conditions.

Molecular details of the yeast frataxin-Isu1 interaction during mitochondrial Fe-S cluster assembly

Frataxin, a conserved nuclear-encoded mitochondrial protein, plays a direct role in iron-sulfur cluster biosynthesis within the ISC assembly pathway. Humans with frataxin deficiency have Friedreich's ataxia, a neurodegenerative disorder characterized by mitochondrial iron overload and disruption in Fe-S cluster synthesis. Biochemical and genetic studies have shown frataxin interacts with the iron-sulfur cluster assembly scaffold protein (in yeast, there are two, Isu1 and Isu2), indicating frataxin plays a direct role in cluster assembly, possibly by serving as an iron chaperone in the assembly pathway. Here we provide molecular details of how yeast frataxin (Yfh1) interacts with Isu1 as a structural module to improve our understanding of the multiprotein complex assembly that completes Fe-S cluster assembly; this complex also includes the cysteine desulfurase (Nfs1 in yeast) and the accessory protein (Isd11), together in the mitochondria. Thermodynamic binding parameters for protein partner and iron binding were measured for the yeast orthologs using isothermal titration calorimetry. Nuclear magnetic resonance spectroscopy was used to provide the molecular details to understand how Yfh1 interacts with Isu1. X-ray absorption studies were used to electronically and structurally characterize how iron is transferred to Isu1 and then incorporated into an Fe-S cluster. These results were combined with previously published data to generate a structural model for how the Fe-S cluster protein assembly complex can come together to accomplish Fe-S cluster assembly.

Human galectin-3 interacts with two anticancer drugs

Human galectin-3 (hGal-3) is a mammalian lectin involved in regulation of RNA splicing, apoptosis, cell differentiation, and proliferation. Multimerized extracellular hGal-3 is thought to crosslink cells by binding to glycoproteins and glycosylated cancer antigens on the cell surface or extracellular matrix. Fluorescence spectroscopy and circular dichroism were used to study the interaction of hGal-3 with two anticancer agents: bohemine and Zn porphyrin (ZnTPPS(4)). The dissociation constant (k(D)) for binding of bohemine with hGal-3 was k(D) 0.23+/-0.05 microM. The hyperbolic titration curve indicated the presence of a single bohemine binding site. The binding of ZnTPPS(4) to hGal-3 (with and without lactose) is of high affinity having k(D)=0.18-0.20 microM and is not inhibited by lactose, indicating that ZnTPPS(4) and carbohydrate bind different sites. Circular dichroism spectra of the hGal-3 complexes suggested that the binding of the hydrophobic compounds changed the hGal-3 secondary structure. In summary, we show that two compounds with anticancer activity, bohemine and ZnTPPS(4), have high affinity for hGal-3 at a site that is distinct from its carbohydrate site. Since hGal-3 binds to several carbohydrate cancer antigens, the results suggest that it may have utility in the targeted delivery of drugs for cancer.

Increase in surface hydrophobicity of the cataract-associated P23T mutant of human gammaD-crystallin is responsible for its dramatically lower, retrograde solubility

The cataract-associated Pro23 to Thr (P23T) mutation in human gammaD-crystallin (HGD) has a variety of phenotypes and is geographically widespread. Therefore, there is considerable interest in understanding the molecular basis of cataract formation due to this mutation. We showed earlier [Pande, A., et al. (2005) Biochemistry 44, 2491-2500] that the probable basis of opacity in this case is the severely compromised, retrograde solubility and aggregation of P23T relative to HGD. The dramatic solubility change occurs even as the structure of the mutant protein remains essentially unchanged in vitro. We proposed that the retrograde solubility and aggregation of P23T were mediated by net hydrophobic, protein-protein interactions. On the basis of these initial findings for P23T and related mutants, and the subsequent finding that they show atypical phase behavior [McManus, J. J., et al. (2007) Proc. Natl. Acad. Sci. U.S.A. 104, 16856-16861], we concluded that the protein clusters formed in solutions of the mutant proteins were held together by net hydrophobic, anisotropic interactions. Here we show, using chemical probes, that the surface hydrophobicities of these mutants are inversely related to their solubility. Furthermore, by probing the isolated N-terminal domains of HGD and P23T directly, we find that the increase in the surface hydrophobicity of P23T is localized in the N-terminal domain. Modeling studies suggest the presence of sticky patches on the surface of the N-terminal domain that could be engaged in the formation of protein clusters via hydrophobic protein-protein interactions. This work thus provides direct evidence of the dominant role played by net hydrophobic and anisotropic protein-protein interactions in the aggregation of P23T.

ANS binding reveals common features of cytotoxic amyloid species

Oligomeric assemblies formed from a variety of disease-associated peptides and proteins have been strongly associated with toxicity in many neurodegenerative conditions, such as Alzheimer's disease. The precise nature of the toxic agents, however, remains still to be established. We show that prefibrillar aggregates of E22G (arctic) variant of the Abeta(1-42) peptide bind strongly to 1-anilinonaphthalene 8-sulfonate and that changes in this property correlate significantly with changes in its cytotoxicity. Moreover, we show that this phenomenon is common to other amyloid systems, such as wild-type Abeta(1-42), the I59T variant of human lysozyme and an SH3 domain. These findings are consistent with a model in which the exposure of hydrophobic surfaces as a result of the aggregation of misfolded species is a crucial and common feature of these pathogenic species.

The structural intolerance of the PrP alpha-fold for polar substitution of the helix-3 methionines

The conversion of the cellular prion protein (PrP(C)) into its disease-associated form (PrP(Sc)) involves a major conformational change and the accumulation of sulfoxidized methionines. Computational and synthetic approaches have shown that this change in the polarity of M206 and M213 impacts the C-terminal domain native alpha-fold allowing the flexibility required for the structural conversion. To test the effect in the full-length molecule with site-specificity, we have generated M-to-S mutations. Molecular dynamics simulations show that the replacement indeed perturbs the native state. When this mutation is placed at the conserved methionines of HaPrP(23-231), only substitutions at the Helix-3 impair the alpha-fold, stabilizing a non-native state with perturbed secondary structure, loss of native tertiary contacts, increased surface hydrophobicity, reduced thermal stability and an enhanced tendency to aggregate into protofibrillar polymers. Our work supports that M206 and M213 function as alpha-fold gatekeepers and suggests that their redox state regulate misfolding routes.

Impact of fluorescent probes on albumin sorption profiles to ophthalmic biomaterials

Bovine serum albumin (BSA) was conjugated to three organic fluorescent probes, 5-(4,6-dichloro-s-triazin-2-ylamino)fluorescein hydrochloride (DTAF), Rhodamine B isothiocyanate (RITC), and Lucifer yellow VS (LY). The protein sorption profile to one pHEMA-based (etafilcon A) and three silicone hydrogel (SH) contact lens types (lotrafilcon B, balafilcon A and senofilcon A) was determined using confocal laser scanning microscopy. In addition, all lenses were incubated in dye solutions containing the fluorescent probe alone; and in a separate experiment BSA accumulation was quantified using radiolabeling. The different fluorescent conjugates showed similar sorption profiles for the pHEMA-based lens, but marked differences for all SH lenses. Lotrafilcon B accumulated more protein on the surface as compared to the matrix, independent of the fluorescent probe used for conjugation. Protein sorption varied for senofilcon A, with DTAF-BSA sorbing primarily to the surface region, while the other conjugates penetrated in equal amounts into the matrix. Balafilcon A exhibited smaller differences between conjugates, with LY-BSA allowing the protein to fully penetrate the matrix, while the other conjugates showed minor surface adsorption. Sorption curves of unbound dyes were often similar compared to the conjugated results. BSA profiles to pHEMA-based and silicone hydrogel lenses were highly dependent on the fluorescent probe used and none of the probes accurately reflected quantitative protein levels for the lens materials investigated.

The sacsin repeating region (SRR): a novel Hsp90-related supra-domain associated with neurodegeneration

Protein supra-domains are defined as recurring arrangements of two or three domains present adjacent to each other along a polypeptide chain. Such combinations have novel functions beyond those of the individual partner domains that compose them, which can exist in isolation. Here, we describe a new type of large supra-domain (approximately 360 residues) in which one of the component partners (approximately 200 residues) appears to be incapable of existing in a context other than immediately adjacent to the C-terminus of the well-characterized Hsp90-like ATPase domain. We found that this supra-domain has a broad phylogenetic distribution, with examples in Archaea, Bacteria, and Eukarya. There is strong selective pressure for this arrangement to occur as part of repeated regions of unprecedented length. We identified multiple strategies of convergent evolution to attain such configurations. In humans, this supra-domain is present in triplicate at the N-terminus of the protein sacsin (4579 residues), mutated in the neurodegenerative disorder known as spastic ataxia of Charlevoix-Saguenay, and thus, we termed it "sacsin repeating region" (SRR). Biochemical characterization demonstrated that SRRs possess ATPase activity, which appears to be a requirement for sacsin function, as a disease-causing mutation leads to an alternate conformation completely incapable of hydrolyzing ATP. We also found evidence of a convergent evolutionary strategy to place SRRs in proteins containing C-terminal J domains, which we demonstrated here to be capable of stimulating the intrinsic ATPase activity of Hsp70. Our sequence and biochemical analyses indicate that SRRs necessitate nucleotide hydrolysis for their function, provided by the common Hsp90 ATPase domain, which, when coupled to the unique adjacent sequence, may give rise to a novel activity related to protein quality control.

Changing the solvent accessibility of the prion protein disulfide bond markedly influences its trafficking and effect on cell function

Prion diseases are fatal transmissible neurodegenerative diseases that result from structural conversion of the prion protein into a disease-associated isoform. The prion protein contains a single disulfide bond. Our analysis of all NMR structures of the prion protein (total of 440 structures over nine species) containing an explicit disulfide bond reveals that the bond exists predominantly in a stable low-energy state, but can also adopt a high-energy configuration. The side chains of two tyrosine residues and one phenylalanine residue control access of solvent to the disulfide bond. Notably, the side chains rotate away from the disulfide bond in the high-energy state, exposing the disulfide bond to solvent. The importance of these aromatic residues for protein function was analysed by mutating them to alanine residues and analysing the properties of the mutant proteins using biophysical and cell biological approaches. Whereas the mutant protein behaved similarly to wild-type prion protein in recombinant systems, the mutants were retained in the endoplasmic reticulum of mammalian cells and degraded by the proteasomal system. The cellular behaviour of the aromatic residue mutants was similar to the cellular behaviour of a disulfide bond mutant prion protein in which the cysteine residues were replaced with alanine, a result which is consistent with an unstable disulfide bond in the aromatic residue mutants. These observations suggest that the conformation of the prion protein disulfide bond may have implications for correct maturation and function of this protein.

Exposure of hydrophobic surfaces initiates aggregation of diverse ALS-causing superoxide dismutase-1 mutants

The copper-zinc superoxide dismutase-1 (SOD1) is a highly structured protein and, a priori, one of the least likely proteins to be involved in a misfolding disease. However, more than 140, mostly missense, mutations in the SOD1 gene cause aggregation of the affected protein in familial forms of amyotrophic lateral sclerosis (ALS). The remarkable diversity of the effects of these mutations on SOD1 properties has suggested that they promote aggregation by a variety of mechanisms. Experimental assessment of surface hydrophobicity using a sensitive fluorescent-based assay, revealed that diverse ALS-causing mutations provoke SOD1 aggregation by increasing their propensity to expose hydrophobic surfaces. These findings could not be anticipated from analysis of the amino acid sequence. Our results uncover the biochemical nature of the misfolded aggregation-prone intermediate and reconcile the seemingly diverse effects of ALS-causing mutations into a unifying mechanism. Furthermore, the method we describe here will be useful for investigating and interfering with aggregation of various proteins and thereby provide insight into the molecular mechanisms underlying many neurodegenerative diseases.

Self-assembly mechanism for a naphthalene-dipeptide leading to hydrogelation

Suitably functionalized dipeptides have been shown to be effective hydrogelators. The design of the hydrogelators and the mechanism by which hydrogelation occurs are both currently not well understood. Here, we have utilized the hydrolysis of glucono-delta-lactone to gluconic acid as a means of adjusting the pH in a naphthalene-alanylvaline solution allowing the specific targeting of the final pH. In addition, this method allows the assembly process to be characterized. We show that assembly begins as charge is removed from the C-terminus of the dipeptide. The removal of charge allows lateral assembly of the molecules leading to pi-pi stacking (shown by CD) and beta-sheet formation (as shown by IR and X-ray fiber diffraction). This leads to the formation of fibrous structures. Electron microscopy reveals that thin fibers form initially, with low persistence length. Lateral association then occurs to give bundles of fibers with higher persistence length. This results in the initially weak hydrogel becoming stronger with time. The final mechanical properties of the hydrogels are very similar irrespective of the amount of GdL added; rather, the time taken to achieving the final gel is determined by the GdL concentration. However, differences are observed between the networks under strain, implying that the kinetics of assembly do impart different final materials' properties. Overall, this study provides detailed understanding of the assembly process that leads to hydrogelation.

Efficient UV detection of protein crystals enabled by fluorescence excitation at wavelengths longer than 300 nm

It is well known that most proteins and many other biomolecules fluoresce when illuminated with UV radiation, but it is also commonly accepted that utilizing this property to detect protein crystals in crystallization setups is limited by the opacity of the materials used to contain and seal them. For proteins, this fluorescence property arises primarily from the presence of tryptophan residues in the sequence. Studies of protein crystallization results in a variety of setup configurations show that the opacity of the containment hardware can be overcome at longer excitation wavelengths, where typical hardware materials are more transparent in the UV, by the use of a powerful UV-light source that is effective in excitation even though not at the maximum of the excitation response. The results show that under these circumstances UV evaluation of crystallization trials and detection of biomolecular crystals in them is not limited by the hardware used. It is similarly true that a deficiency in tryptophan or another fluorescent component that limits the use of UV light for these purposes can be effectively overcome by the addition of fluorescent prostheses that bind to the biomolecule under study. The measurements for these studies were made with a device consisting of a potent UV-light source and a detection system specially adapted (i) to be tunable via a motorized and software-controlled absorption-filter system and (ii) to convey the excitation light to the droplet or capillary hosting the crystallization experiment by quartz-fibre light guides.

Beta-peptide bundles with fluorous cores

We reported recently that certain beta-peptides self-assemble spontaneously into cooperatively folded bundles whose kinetic and thermodynamic metrics mirror those of natural helix bundle proteins. The structures of four such beta-peptide bundles are known in atomic detail. These structures reveal a solvent-sequestered, hydrophobic core stabilized by a unique arrangement of leucine side chains and backbone methylene groups. Here we report that this hydrophobic core can be re-engineered to contain a fluorous subdomain while maintaining the characteristic beta-peptide bundle fold. Like alpha-helical bundles possessing fluorous cores, fluorous beta-peptide bundles are stabilized relative to hydrocarbon analogues and undergo cold denaturation. Beta-peptide bundles with fluorous cores represent the essential first step in the synthesis of orthogonal protein assemblies that can sequester selectively in an interstitial membrane environment.

The molecular chaperone alpha-crystallin as an excipient in an insulin formulation

Purpose

To investigate insulin fibrillation under accelerated stress conditions in the presence of a novel excipient, the molecular chaperone α-crystallin, in comparison with common excipients.

Methods

To induce fibrillation, recombinant human insulin (0.58 mg ml⁻¹) formulations without excipient or with bovine α-crystallin (0.01–0.2 mg ml⁻¹), human serum albumin (1–5 mg ml⁻¹), sucrose (10–100 mg ml⁻¹) or polysorbate 80 (0.075–0.3 mg ml⁻¹) were subjected to stirring stress in a fluorescence well plate reader and formulation vials. Protein fibrillation was monitored by thioflavin T. The formulations were further characterized by size-exclusion chromatography, light obscuration, UV/Vis and circular dichroism spectroscopy.

Results

In both methods, insulin formed thioflavin T-binding species, most likely fibrils. Addition of α-crystallin in the well plate assay greatly improved insulin’s resistance to fibrillation, measured as a 6-fold increase in fibrillation lag time for the lowest and 26-fold for the highest concentration used, whereas all other excipients showed only a marginal increase in lag time. The stabilizing effect of α-crystallin was shown by all characterization techniques used.

Conclusions

The effect of α-crystallin on insulin’s physical stability outperforms that of commonly used excipients. α-Crystallin is proposed to bind specifically to pre-fibrillation species, thereby inhibiting fibrillation. This makes α-crystallin an interesting excipient for proteins with propensity to fibrillate.

Aggregation of a multidomain protein: a coagulation mechanism governs aggregation of a model IgG1 antibody under weak thermal stress

Using an IgG1 antibody as a model system, we have studied the mechanisms by which multidomain proteins aggregate at physiological pH when incubated at temperatures just below their lowest thermal transition. In this temperature interval, only minor changes to the protein conformation are observed. Light scattering consistently showed two coupled phases: an initial fast phase followed by several hours of exponential growth of the scattered intensity. This is the exact opposite of the lag-time behavior typically observed in protein fibrillation. Dynamic light scattering showed the rapid formation of an aggregate species with a hydrodynamic radius of about 25 nm, which then increased in size throughout the experiment. Theoretical analysis of our light scattering data showed that the aggregate number density goes through a maximum in time providing compelling evidence for a coagulation mechanism in which aggregates fuse together. Both the analysis as well as size-exclusion chromatography of incubated samples showed the actual increase in aggregate mass to be linear and reach saturation long before all molecules had been converted to aggregates. The CH2 domain is the only domain partly unfolded in the temperature interval studied, suggesting a pivotal role of this least stable domain in the aggregation process. Our results show that for multidomain proteins at temperatures below their thermal denaturation, transient unfolding of a single domain can prime the molecule for aggregation, and that the formation of large aggregates is driven by coagulation.

Misconceptions over Förster resonance energy transfer between proteins and ANS/bis-ANS: Direct excitation dominates dye fluorescence

Our aim was to disprove the widespread misconception that Förster resonance energy transfer (FRET) is the only explanation for observing fluorescence from ANS (8-anilino-1-naphthalenesulfonic acid) and bis-ANS (4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid, dipotassium salt) following excitation at 280nm in the presence of protein. From ultraviolet (UV) absorption spectra and fluorescence emission spectra of bis-ANS and ANS in buffer and ethanol, direct excitation at 280nm was found to be the dominant mechanism for the resulting dye fluorescence. Furthermore, Tyr/Trp quenching studies were performed for solutions of N-acetyl-l-tryptophanamide, heat-stressed immunoglobulin G (IgG), and bovine serum albumin (BSA) by monitoring changes in steady state fluorescence spectra and time-resolved fluorescence decays as a function of dye concentration. Stronger quenching of the intrinsic BSA and IgG fluorescence in steady state than in time-resolved fluorescence by bis-ANS and ANS pointed toward static quenching being the dominant mechanism in addition to dynamic quenching and/or FRET. In conclusion, one should consider the role of direct excitation of ANS and bis-ANS at 280nm to ensure a proper interpretation of fluorescence signals resulting from dye-protein interactions. When ANS or bis-ANS is to be used for protein characterization, we recommend selectively exciting the dyes at the higher absorption wavelength maximum (370 or 385nm, respectively).

Fluorescent study of human blood plasma albumin alterations induced by ionizing radiation

The use of hydrophobic fluorescent probe ABM (benzanthrone derivative) and albumin autofluorescence allowed show conformational alterations in Chernobyl clean-up workers blood plasma. Results obtained in 1996-1997 suggest that acidic expansion of plasma albumin takes place. Latest data (2006-2008) result in splitting of albumin alterations onto two stages - acidic expansion and N-F transition. The N-F transition is accompanied by the blue shift of fluorescence spectra and dehydration of tryptophanyl region of albumin molecule. In 2007 obtained.patterns of ABM spectra had never been previously seen in examined healthy individuals or patients with tuberculosis, multiple sclerosis, rheumatoid arthritis, etc. Patterns of ABM fluorescence spectra are associated with conformational changes of blood plasma albumin. The use of probe ABM and albumin auto-fluorescence allowed show conformational alterations in albumin of Chernobyl clean-up workers blood plasma. It is necessary to note that all investigated parameters significantly differ in observed groups of patients. These findings reinforce our understanding that the blood plasma albumin is a significant biological target of radiation. It may be concluded that fluorescence characteristics are representative of radiation induced albumin alterations and its carrier function.

Physical instability, aggregation and conformational changes of recombinant human bone morphogenetic protein-2 (rhBMP-2)

The influence of two different pH values on the physical stability of recombinant human bone morphogenetic protein-2 (rhBMP-2) in aqueous solution was evaluated in the present work. RhBMP-2 in solution at pH 4.5 or 6.5 was characterized by intrinsic and extrinsic (Nile Red and 1,8-ANS) fluorescence spectroscopy, 90 degrees light-scattering and transmission electron microscopy (TEM). Compared to the pH 4.5 solution, rhBMP-2 at pH 6.5 had (i) a stronger intrinsic fluorescence intensity, (ii) a longer fluorescence lifetime, (iii) a stronger 90 degrees light-scattering intensity, (iv) a stronger Nile Red fluorescence intensity, (v) a higher Nile Red fluorescence anisotropy, (vi) a lower 1,8-ANS fluorescence intensity, (vii) a higher 1,8-ANS fluorescence anisotropy and (viii) a longer 1,8-ANS fluorescence lifetime. Electron microscopy showed that rhBMP-2 at pH 4.5 contained aggregates of about 100 nm in diameter. More and larger protein aggregates (0.1-2 microm) were observed in solution at pH 6.5. Taken together, these results indicate conformational changes and increased aggregation of rhBMP-2 at pH 6.5 compared to pH 4.5, demonstrating a strong influence of pH on rhBMP-2 physical stability. These observations must be considered when developing a delivery system for rhBMP-2.

Revealing of Saccharomyces cerevisiae yeast cell wall proteins capable of binding thioflavin T, a fluorescent dye specifically interacting with amyloid fibrils

Proteins binding thioflavin T leading to its specific fluorescence were discovered in a fraction of noncovalently bound Saccharomyces cerevisiae yeast cell wall mannoproteins. Thioflavin-binding proteins display high resistance to trypsin digestion in solution. These data are the first experimental evidence for the presence of proteins whose properties are characteristic of amyloids in yeast cell wall, except for data on glucanotransferase Bgl2p that has amyloid properties. Our data suggest the anchoring of these proteins in the cell wall by a trypsin-sensitive part of the protein molecule. Experiments with a mutant strain devoid of the BGL2 gene suggest the compensation of absent amyloid-like protein Bgl2p by increase in contents of thioflavin-binding proteins in the cell wall.

Sonochemical synthesis of liquid-encapsulated lysozyme microspheres

Liquid-encapsulated lysozyme microspheres were successfully synthesized using a sonochemical method. The encapsulation of four different liquids, namely, sunflower oil, tetradecane, dodecane and perfluorohexane on the formation, stability and morphology of the lysozyme microspheres was studied. Among the four different liquids used for encapsulation, perfluorohexane-filled microspheres were found to be most stable in the dried state with a narrow size distribution. In order to explore the possibility of encapsulating biofunctional molecules (e.g., drugs) within these microspheres, liquids containing a fluorescent dye (Nile red) were encapsulated and the ultrasound-induced release of these dye-loaded liquids was studied. The fluorescence data for the liquid-filled lysozyme microspheres demonstrated the potential use of the sonochemical technique for synthesizing these "vehicles" for the encapsulation and the controlled delivery of dyes, flavours, fragrances or drugs.

Crystal structure of thioflavin-T and its binding to amyloid fibrils: insights at the molecular level

Combining X-ray data on thioflavin-T and theoretical calculations on its binding to a peptide model for Abeta(1-42) fibrils gives evidence of main stabilizing interactions, which influence the dihedral angle between the two moieties of thioflavin-T and thereby its fluorescence properties; these results shed new light on possible strategies for the design of dyes to bind amyloid fibrils more specifically.

Fluorescent molecular rotors as dyes to characterize polysorbate-containing IgG formulations

PURPOSE

The aim was to evaluate fluorescent molecular rotors (DCVJ and CCVJ), which are mainly sensitive to viscosity, for the characterization of polysorbate-containing IgG formulations and compare them to the polarity-sensitive dyes ANS, Bis-ANS and Nile Red.

METHODS

IgG formulations with polysorbate 20 or 80 were stressed below the aggregation temperature and analyzed by steady-state and time-resolved fluorescence and by HP-SEC with UV and fluorescent dye detection (Bis-ANS and CCVJ). Furthermore, commercial protein preparations of therapeutic proteins (Enbrel 50 mg, Humira 40 mg and MabThera 100 mg) were aggregated accordingly and analyzed with CCVJ fluorescence and HP-SEC.

RESULTS

Contrarily to (Bis-)ANS and Nile Red, the molecular rotors DCVJ and CCVJ showed low background fluorescence in polysorbate-containing buffers. Time-resolved fluorescence experiments confirmed the steady-state fluorescence data. Both DCVJ and CCVJ showed enhanced fluorescence intensity for aggregated IgG formulations and were suitable for the characterization of polysorbate-containing IgG formulations in steady-state fluorescence and HP-SEC with dye detection (CCVJ). CCVJ was capable of detecting thermally induced aggregation in the commercial polysorbate-containing products Enbrel 50 mg, Humira 40 mg and MabThera 100 mg.

CONCLUSION

Fluorescent molecular rotors are suitable probes to detect aggregation in polysorbate-containing IgG formulations.

Comparative study on heat stability of camel and bovine apo and holo α-lactalbumin

The stability of camel α-lactalbumin (α-la) against heat denaturation was measured, using circular dichroism (CD) and fluorescence spectroscopy, as well as differential scanning calorimetry (DSC). The experiments were performed in the presence of saturating concentrations of calcium as well as in the presence of EDTA, yielding to the apo form of α-la. The change in heat capacity (ΔCp) suggests a greater contribution of hydrophobic interactions to the stability of holo camel α-la than in its bovine counterpart. Overall the results obtained in this study suggest a greater stability of camel α-la than the bovine protein in both holo and apo states. Also CD experiments showed similar secondary structure for camel and bovine α-la and secondary structure of camel α-la was better preserved than that of bovine α-la during heat denaturation. The differences in thermal stability between the proteins from two species can be primarily ascribed to the difference in the quantity of hydrophobic interactions involved in their folding.

The p53 core domain is a molten globule at low pH: functional implications of a partially unfolded structure

p53 is a transcription factor that maintains genome integrity, and its function is lost in 50% of human cancers. The majority of p53 mutations are clustered within the core domain. Here, we investigate the effects of low pH on the structure of the wild-type (wt) p53 core domain (p53C) and the R248Q mutant. At low pH, the tryptophan residue is partially exposed to the solvent, suggesting a fluctuating tertiary structure. On the other hand, the secondary structure increases, as determined by circular dichroism. Binding of the probe bis-ANS (bis-8-anilinonaphthalene-1-sulfonate) indicates that there is an increase in the exposure of hydrophobic pockets for both wt and mutant p53C at low pH. This behavior is accompanied by a lack of cooperativity under urea denaturation and decreased stability under pressure when p53C is in acidic pH. Together, these results indicate that p53C acquires a partially unfolded conformation (molten-globule state) at low pH (5.0). The hydrodynamic properties of this conformation are intermediate between the native and denatured conformation. ¹H-¹⁵N HSQC NMR spectroscopy confirms that the protein has a typical molten-globule structure at acidic pH when compared with pH 7.2. Human breast cells in culture (MCF-7) transfected with p53-GFP revealed localization of p53 in acidic vesicles, suggesting that the low pH conformation is present in the cell. Low pH stress also tends to favor high levels of p53 in the cells. Taken together, all of these data suggest that p53 may play physiological or pathological roles in acidic microenvironments.

Can the fluorescence of green fluorescent protein chromophore be related directly to the nativity of protein structure?

In studies of green fluorescence protein (GFP) or other proteins with the use of GFP as a marker, the fluorescence of GFP is for the most part related directly to the nativity of its structure. Naturally, such a relation does exist since the chromophore of this protein is formed autocatalytically only just after GFP acquires its native structure. However, the fluorescence method may not yield reliable information on protein structure when studying renaturation and denaturation of this protein (with the formed chromophore). Using proteolysis, denaturant gradient gel electrophoresis and circular dichroism, we demonstrate herein that at major disturbances of the native structure of protein GFP-cycle3 the intensity of fluorescence of its chromophore can change insignificantly. In other words, the chromophore fluorescence does not reliably mirror alterations in protein structure. Since the main conclusions of this study are especially qualitative, it can be suggested that during renaturation/denaturation of wild-type GFP and its "multicolored" mutants their fluorescence is also not always associated with the changes in the structure of these proteins.

Evolution of stability in a cold-active enzyme elicits specificity relaxation and highlights substrate-related effects on temperature adaptation

Molecular aspects of thermal adaptation of proteins were studied by following the co-evolution of temperature dependence, conformational stability, and substrate specificity in a cold-active lipase modified via directed evolution. We found that the evolution of kinetic stability was accompanied by a relaxation in substrate specificity. Moreover, temperature dependence and selectivity turned out to be mutually dependent. While the wild-type protein was strictly specific for short-chain triglycerides (C4) in the temperature range 10-50 degrees C and displayed highest activity in the cold, its stabilized variant was able to accept C8 and C12 molecules and its selectivity was temperature dependent. We could not detect any improvement in the overall structural robustness of the mutant when the structure was challenged by temperature or chemical denaturants. There is, however, strong evidence for local stabilization effects in the active-site region provided by two independent approaches. Differential scanning fluorimetry revealed that the exposure of hydrophobic patches (as the active site is) precedes denaturation, and molecular dynamics simulations confirmed that stability was obtained by restriction of the mobility of the lid, a flexible structure that regulates the access to the enzyme active site and influences its stability. This reduction of lid movements is suggested to be accompanied by a concomitant increase in the mobility of other protein regions, thus accounting for the observed broadening of substrate specificity.