Acid-induced unfolding of brain-derived neurotrophic factor results in the formation of a monomeric "a state"

Amyloid aggregation and secondary structure changes of liver cystatin: Acidic denaturation and TFE induced studies

A cysteine proteinase inhibitor has been purified by affinity chromatography from the liver of buffalo. Liver cystatin is subjected to incubation at low pH with co-solvent TFE, where we have studied the effect on the conformation, activity and tendency to form aggregates or fibrils. ANS fluorescence was used to study conformational changes. The fibril formation and aggregation was studied using ThT assay, CD, FTIR and fluorescence spectroscopy. At pH 3.0 there was no fibril formation though aggregates were formed but in presence of TFE fibrils appeared. At pH 2.0 and 1.0, TFE induced rapid fibril formation compared to only acid induced state as assessed by Thioflavin T (ThT) fluorescence.TFE stabilized each of the three acid induced intermediates at predenaturational concentrations (20%) and accelerated fibril formation. Solvent conditions had a profound effect on the tendency of liver cystatin to produce fibrils and aggregation.Communicated by Ramaswamy H. Sarma.

ATP-NGF-complex, but not NGF, is the neuroprotective ligand

We have shown previously that nerve growth factor (NGF) requires only low nanomolar ATP concentrations in the cell culture medium to protect cortical rat neurons (CRN) from cellular damage induced by staurosporine (STS). We have also demonstrated before that NGF and other growth factors form stable non-covalent complexes with ATP. Here we demonstrated that 8N(1)ATP-NGF, but not NGF, protected CRN against damage. The photo-reactive ATP derivative 8N(3)ATP was incubated with NGF and was trapped in its position by UV irradiation forming a covalent bond. The cross-link with a molar ratio of 1:1 (8N(1)ATP:NGF) was confirmed by mass spectrometry. Circular dichroism experiments revealed that 8N(1)ATP altered the secondary structure of NGF in the same way as ATP did. Covalently bound 8N(1)ATP-NGF was shown to be stable in the presence of the ATP-hydrolyzing enzyme alkaline phosphatase while the non-covalent ATP-NGF-complex dissociated with the removal of free ATP from the solution. 8N(1)ATP-NGF protected CRN against damage by STS independently of free ATP in the culture medium. These results suggest that the ATP-NGF-complex, but not NGF, is the active ligand.

Binding of ATP to nerve growth factor: characterization and relevance for bioactivity

Growth factors and their mechanisms of action have been studied extensively. However, it remained widely unrecognized that binding of ATP to growth factors is a prerequisite for their bioactivity. Here we demonstrated the binding of ATP to nerve growth factor (NGF) as well as its relevance for neuroprotection. By using mass spectrometry-based methodology we identified one or two molecules of ATP as being bound to NGF. To test neuroprotective activity of NGF we used primary cultures of rat cortical neurons damaged by staurosporine. ATP was indispensable for the neuroprotective effect of NGF. When the ATP concentration in the culture medium was reduced below approximately 2 nM by adding alkaline phosphatase (AP) or ATPase the neuroprotective activity of NGF was abolished. Site-directed mutagenesis within the heparin-binding domain (HBD) of NGF abolished ATP-binding and the neuroprotective effect. Thus, NGF has to bind ATP to be capable of protecting neurons.

Size-exclusion chromatography with on-line light scattering

This unit describes the use of size-exclusion chromatography with on-line light scattering, UV absorbance, and refractive index detectors (SEC-LS/UV/RI) to determine: (a) the molecular weight of simple proteins containing no carbohydrates, (b) the molecular weight of glycoproteins, and (c), most importantly, the molecular weight and stoichiometry of protein-protein complexes or protein-carbohydrate complexes. Multiangle light scattering is also discussed.

Molecular characterization and sex-specific tissue expression of prolactin, somatolactin and insulin-like growth factor-I in yellow perch (Perca flavescens)

The cDNA sequences encoding prolactin (PRL), somatolactin (SL) and insulin-like growth factor-I (IGF-I) genes of the yellow perch were obtained. Brain, pituitary, gill, heart, liver, stomach, kidney, spleen, muscle and gonad tissues were analyzed from both male and female adult yellow perch for sex-specific tissue expression. The full length cDNA of yellow perch PRL consists of 2306 bp and PRL expression was highest in the yellow perch pituitary with low to moderate expression in other tissues including brain, gill and post-vitellogenic oocytes. The full length cDNA of yellow perch SL consists of 1589 bp and SL expression was highest in the yellow perch pituitary with low to moderate expression in other tissues including brain, gill, liver, stomach, spleen and kidney. The full length cDNA of yellow perch IGF-Ib consists of 814 bp and tissue expression analysis of yellow perch IGF-I revealed a second yellow perch transcript (IGF-Ia) that is 81 nucleotides smaller. Both IGF-Ib and IGF-Ia had the greatest expression in liver tissue with moderate expression in brain, spleen and kidney tissues of both sexes. These sequences are valuable molecular tools which can be used in future studies investigating the basis for sexually dimorphic growth in yellow perch.

The folding of dimeric cytoplasmic malate dehydrogenase. Equilibrium and kinetic studies

Porcine heart cytoplasmic malate dehydrogenase (s-MDH) is a dimeric protein (2 x 35 kDa). We have studied equilibrium unfolding and refolding of s-MDH using activity assay, fluorescence, far-UV and near-UV circular dichroism (CD) spectroscopy, hydrophobic probe-1-anilino-8-napthalene sulfonic acid binding, dynamic light scattering, and chromatographic (HPLC) techniques. The unfolding and refolding transitions are reversible and show the presence of two equilibrium intermediate states. The first one is a compact monomer (MC) formed immediately after subunit dissociation and the second one is an expanded monomer (ME), which is little less compact than the native monomer and has most of the characteristic features of a 'molten globule' state. The equilibrium transition is fitted in the model: 2U <--> 2M(E) <--> 2M(C) <--> D. The time course of kinetics of self- refolding of s-MDH revealed two parallel folding pathways [Rudolph, R., Fuchs, I. & Jaenicke, R. (1986) Biochemistry 25, 1662-1669]. The major pathway (70%) is 2U-->2M*-->2M-->D, the rate limiting step being the isomerization of the monomers (K1 = 1.7 x 10(-3) s(-1)). The minor pathway (30%) involves an association step leading to the incorrectly folding dimers, prior to the very slow D*-->D folding step. In this study, we have characterized the folding-assembly pathway of dimeric s-MDH. Our kinetic and equilibrium experiments indicate that the folding of s-MDH involves the formation of two folding intermediates. However, whether the equilibrium intermediates are equivalent to the kinetic ones is beyond the scope of this study.

Sodium chloride enhances the storage and conformational stability of BDNF and PEG-BDNF

PURPOSE

BDNF, a noncovalent homodimer, was modified by covalently attaching polyethylene glycol (PEG) with an average molecular weight of 20kDa to the N-terminal methionine. Stability of modified BDNF (PEG-BDNF) in aqueous solution was compared to BDNF after storage at elevated temperature in the presence and absence of NaCl.

METHODS

SDS-PAGE. Light Scattering and Size Exclusion Chromatography were used to assess conformational stability and chemical degradation. In addition, CD spectroscopy was used to follow changes in secondary and tertiary structures upon thermal stress of the protein.

RESULTS

NaCl containing formulations are more stable than NaCl-free formulations. In NaCl-free formulations, the main degradation product of BDNF and PEG-BDNF had a molecular weight of monomer that was more chemically degraded than the dimer. Additionally, the degradation of PEG-BDNF occurred at an accelerated rate compared to BDNF in NaCl-free environments.

CONCLUSIONS

The addition of NaCl to formulations enhances the shelf-life and conformational stability of both BDNF and PEG-BDNF.

A common mechanism for recombinant human NGF, BDNF, NT-3, and murine NGF slow unfolding

The recombinant human nerve growth factor (hNGF), brain-derived neurotrophic factor (BDNF), neurotrophin-3 (NT-3), neurotrophin 4/5 (NT4/5), and murine NGF (mNGF) dimers all undergo rapid unfolding and dissociation to monomer in GdnHCl. Fluorescence spectroscopy, reversed-phase high-performance liquid chromatography, and size-exclusion chromatography were used to show that this monomer M1 converts slowly to a more fully unfolded monomer, M2, by a first order process with half-lives of 22, 2.5, 1.6, and 0.73 h for hNGF, mNGF, NT-3, and BDNF, respectively, at 25 degrees C. Linear Arrhenius plots for the conversion of M1 to M2 yielded activation energies of 27, 22, 24, and 24 kcal/mol for hNGF, mNGF, NT-3, and BDNF, respectively. The refolding of these neurotrophins from 5 M GdnHCl was also first order with NT-3 the slowest to refold and BDNF the fastest. Threading of the N-terminus out through the cystine-knot loop present in each of these proteins is proposed as the slow step in unfolding. The number of amino acids in the cystine-knot loop (14 for hNGF, mNGF, NT-3, and BDNF; 21 for NT4/5), and the number and position of the proline residues in this loop (2 for hNGF; 1 for mNGF, NT-3, BDNF, and NT4/5) correlate with the relative rates of unfolding. The smaller the loop and the greater the number of prolines, the more hindered and slower the unfolding.

Evidence of stable monomeric species in the unfolding of Cu,Zn superoxide dismutase from Photobacterium leiognathi

The equilibrium unfolding process of Photobacterium leiognathi Cu,Zn superoxide dismutase has been quantitatively monitored through circular dichroism (CD) and fluorescence spectroscopy, upon increasing the guanidinium hydrochloride concentration. The study has been undertaken for both the holo- and the copper-free derivative to work out the role of copper in protein stability. In both cases the unfolding was reversible. The denaturation curve derived from CD and fluorescence spectroscopy was not coincident, suggesting that the denaturation process occurs through a three-state model with formation of an intermediate monomeric species. The occurrence of an intermediate species has been unambiguously demonstrated following CD and steady-state fluorescence spectra of the enzyme at various concentrations in presence of a fixed amounts of guanidinium hydrochloride.

Equilibrium and transient intermediates in folding of human macrophage migration inhibitory factor

Acid, guanidinium-Cl and urea denaturations of recombinant human macrophage migration inhibitory factor (MIF) were measured using CD and fluorimetry. The acid-induced denaturation was followed by CD at 200, 222, and 278 nm and by tryptophan fluorescence. All four probes revealed an acid-denatured state below pH 3 which resembled a typical molten globule. The pH transition is not two-state as the CD data at 222 nm deviated from all other probes. Urea and guanidinium-Cl denaturations (pH 7, 25 degrees C) both gave an apparent DeltaGU app H2O of 31 +/- 3 kJ.mol-1 when extrapolated to zero denaturant concentration. However, denaturation transitions recorded by fluorescence (at the same protein concentration) occurred at lower urea or guanidinium-Cl concentrations, consistent with an intermediate in the course of MIF denaturation. CD at 222 nm was not very sensitive to protein concentration (in 10-fold range) even though size-exclusion chromatogryphy (SEC) revealed a dimer-monomer dissociation prior to MIF unfolding. Refolding experiments were performed starting from acid, guanidinium-Cl and urea-denatured states. The kinetics were multiphasic with at least two folding intermediates. The intrinsic rate constant of the main folding phase was 5.0 +/- 0.5 s-1 (36.6 degrees C, pH 7) and its energy of activation 155 +/- 12 kJ.mol-1.

Recombinant rat fibroblast growth factor-16: structure and biological activity

Fibroblast growth factor-16 (FGF-16) is the most recent member of the FGF family to be cloned. Since the biologic activity of rat FGF-16 (rFGF-16) was unknown, and this protein has no apparent signal sequence, we transformed its entire cDNA into Escherichia coli for high-level expression and further characterization of this novel protein. An attempt was made to purify the expressed protein from the supernatant of mechanically lysed cells using sequential cation-exchange chromatography. This resulted in a gradual loss of the protein as precipitate throughout the purification process. In addition to precipitation during purification, sodium dodecyl sulfate polyacrylamide gel electrophoresis revealed that the partially purified materials showed a cluster of protein bands around 20k to 29k. Sequence analysis of the major bands indicated that two N-terminal truncations had occurred, during E. coli fermentation, purification, or both. The largest truncation resulted in the removal of the 34 N-terminal amino acids, including the initiation codon methionine. We cloned d34 rFGF-16, expressed the gene in E. coli, and developed a purification process for this form. Even with this truncated form, precipitation was a problem. We were largely able to overcome this problem, however, by including EDTA throughout the purification process. We have characterized the structure of purified d34 rFGF-16 extensively using circular dichroism, Fourier transform infrared spectroscopy, and sedimentation velocity analysis. These studies revealed that the protein has a distinct tertiary structure, consists primarily of beta-strands, has a weak tendency to self-associate, and is fairly extended. We then performed biologic assays which showed that d34 rFGF-16 induces oligodendrocyte proliferation in vitro, and induces hepatocellular proliferation and increased liver weight in vivo. In summary, FGF-16, a novel FGF family member, has both unique structural and biological properties.

Characterization of the equilibrium intermediates in acid denaturation of human stefin B

Acid-induced denaturation of recombinant human stefin B was followed using circular dichroism (CD) and fluorimetry. By comparing different spectroscopic probes, a number of equilibrium intermediates were detected. In pH denaturation at very low salt concentration (0.03 M NaCl) four states can be distinguished: N - I(N) - I1 - U, where N is the native state, I(N) is a native-like intermediate, I1 is an acid intermediate state with properties of a molten globule and U is the unfolded state. State 1, exhibits no near-ultraviolet CD but has some residual far-ultraviolet CD. It differs from U in its ability to increase fluorescence of 1-anilino-naphthalene 8-sulfonate (ANS). In 0.42 M salt, the pH denaturation is three-state between the dimeric native state N2 and intermediates I(N2) and I2, which are also dimeric according to size-exclusion chromatography. The acid intermediate I2 is more structured than I1: it binds ANS to a lower extent an I1, its Tyr residues are protected from the solvent, it shows some near-ultraviolet CD and its far-ultraviolet CD is even more intense than that for the native state. 1H-NMR spectra confirmed the overall structural features of the acid intermediates. To obtain the enthalpies of unfolding, microcalorimetric measurements were performed under conditions where the acid intermediates are maximally populated (18 degrees C): state I(N) from pH 5.0 to 4.6, 0.03 M salt: state I1 below pH 3.8, 0.42 M salt; and state I1 in equilibrium with I(N) at pH 4.05, 0.03 M salt. Enthalpies of unfolding for states I(N) and I1 were comparable to those of the native state. The enthalpy of unfolding for state I1 could not be determined.

Changes in conformation and stability upon formation of complexes of erythropoietin (EPO) and soluble EPO receptor

Erythropoietin (EPO) is a glycoprotein hormone which belongs to the four-helical-bundle cytokine family and regulates the level of circulating red blood cells. The EPO receptor (EPOR) belongs to the cytokine-receptor family of proteins. While many of the downstream events following receptor/ligand interaction have been defined, both ligand-induced receptor dimerization and conformational changes induced by binding have been implicated as the initial step in signal transduction. In a recent paper [Philo et al. (1996), Biochemistry 38, 1681-1691] we described the formation of both 1:1 and 2:1 EPOR/EPO complexes. In this paper, we examine changes in protein conformation and stability resulting from the formation of both 1:1 and 2:1 complexes of the soluble extracellular domain of EPOR and the recombinant EPO derived from either Chinese hamster ovary cells or from Escherichia coli cells. Occupation of the first binding site results in a slight conformational change that is apparent in both the far- and near-UV circular dichroism spectra. Formation of the 2:1 complex results in an even greater change in conformation which involves the local environment of one or more aromatic amino acids, accompanied perhaps by a small increase in helical content of the complex. This change in local conformation could occur in the EPO molecule, in the EPOR, in both EPOR molecules due to dimerization, or in all molecules in the trimer. The 1:1 complex exhibits increased stability to thermal-induced denaturation relative to the individual protein component; indeed, the E. coli-derived (nonglycosylated) EPO stays folded in the complex at temperatures where the EPO alone would have unfolded and precipitated. Glycosylation of the receptor increases the reversibility of thermal denaturation, but does not affect the temperature at which this unfolding reaction occurs.

Strategies to suppress aggregation of recombinant keratinocyte growth factor during liquid formulation development

Recombinant human keratinocyte growth factor (rhKGF) is a fairly unstable protein, posing a challenging problem for long-term storage. During storage, the protein unfolds at relatively low temperatures and the unfolded proteins aggregate rapidly, leading to the formation of large visible precipitates. Thermal unfolding of rhKGF displays a similar pattern, i.e., unfolding is followed immediately by aggregation as the temperature is increased. As the unfolding and aggregation (precipitation) of rhKGF limit the storage life of the protein, a search for stabilizers to suppress rhKGF unfolding and aggregation has been done by examining the effects of excipients on thermal melting temperature and on the rate of protein aggregation during storage. Sulfated polysaccharides and citrate are found to be effective in increasing the melting temperature of rhKGF or preventing its aggregation. In particular, 0.5% (w/v) heparin and high molecular weight dextran sulfate, and 0.5 M citrate are highly effective, decreasing the rates of rhKGF aggregation by about 50-fold. Other negatively charged small ions, such as phosphate, also have moderate stabilizing effects on rhKGF. A mechanistic study of the aggregation pathway of rhKGF has led to a better understanding of the stabilizing effects of these molecules. Molecules which enhance rhKGF conformational stability are capable of effectively suppressing rhKGF aggregation.

Conformational stability of dimeric proteins: quantitative studies by equilibrium denaturation

The conformational stability of dimeric globular proteins can be measured by equilibrium denaturation studies in solvents such as guanidine hydrochloride or urea. Many dimeric proteins denature with a 2-state equilibrium transition, whereas others have stable intermediates in the process. For those proteins showing a single transition of native dimer to denatured monomer, the conformational stabilities, delta Gu (H2O), range from 10 to 27 kcal/mol, which is significantly greater than the conformational stability found for monomeric proteins. The relative contribution of quaternary interactions to the overall stability of the dimer can be estimated by comparing delta Gu (H2O) from equilibrium denaturation studies to the free energy associated with simple dissociation in the absence of denaturant. In many cases the large stabilization energy of dimers is primarily due to the intersubunit interactions and thus gives a rationale for the formation of oligomers. The magnitude of the conformational stability is related to the size of the polypeptide in the subunit and depends upon the type of structure in the subunit interface. The practical use, interpretation, and utility of estimation of conformational stability of dimers by equilibrium denaturation methods are discussed.

Characterisation of neurotrophin dimers and monomers

When recombinant brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT-3) are purified by reverse-phase chromatography, these neurotrophins elute as two distinct peaks. This is also the case when naturally occurring BDNF is purified from brain tissue. As indicated by gelfiltration experiments, the peaks with shorter retention times correspond to neurotrophin dimers, those with longer retention times to monomers. In contrast, a BDNF mutant with a single amino-acid replacement (Arg-1-->Lys) in the basic processing site common to all neurotrophin precursors elutes as a single peak. This peak is shown by gel-filtration chromatography to consist of dimers with a molecular mass almost twice that of wild-type dimers. N-terminal sequencing indicates an extension of 19 amino acids, including a glycosylated asparagine residue. The biological activity of the BDNF mutant ([R-1K]BDNF) is identical with that of wild-type BDNF when tested in a neuron survival assay. Using this assay, the biological activities of guanidine-hydrochloride-denatured neurotrophin monomers were found to be much lower than that of the dimers, and experiments with NT-3 monomers and NIH3T3 cells expressing trkC suggest that such monomers exist in solution in a conformation that prevents efficient interactions with neurotrophin receptors.