Kinetic study of protein unfolding and refolding using urea gradient electrophoresis

Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions

The functional structure of proteins results from marginally stable folded conformations. Reversible unfolding, irreversible denaturation, and deterioration can be caused by chemical and physical agents due to changes in the physicochemical conditions of pH, ionic strength, temperature, pressure, and electric field or due to the presence of a cosolvent that perturbs the delicate balance between stabilizing and destabilizing interactions and eventually induces chemical modifications. For most proteins, denaturation is a complex process involving transient intermediates in several reversible and eventually irreversible steps. Knowledge of protein stability and denaturation processes is mandatory for the development of enzymes as industrial catalysts, biopharmaceuticals, analytical and medical bioreagents, and safe industrial food. Electrophoresis techniques operating under extreme conditions are convenient tools for analyzing unfolding transitions, trapping transient intermediates, and gaining insight into the mechanisms of denaturation processes. Moreover, quantitative analysis of electrophoretic mobility transition curves allows the estimation of the conformational stability of proteins. These approaches include polyacrylamide gel electrophoresis and capillary zone electrophoresis under cold, heat, and hydrostatic pressure and in the presence of non-ionic denaturing agents or stabilizers such as polyols and heavy water. Lastly, after exposure to extremes of physical conditions, electrophoresis under standard conditions provides information on irreversible processes, slow conformational drifts, and slow renaturation processes. The impressive developments of enzyme technology with multiple applications in fine chemistry, biopharmaceutics, and nanomedicine prompted us to revisit the potentialities of these electrophoretic approaches. This feature review is illustrated with published and unpublished results obtained by the authors on cholinesterases and paraoxonase, two physiologically and toxicologically important enzymes.

Sensitive detection of proteins in polyacrylamide gel via isatoic anhydride derivatization: Introduction of a low-cost fluorescent prelabeling procedure

Here, we introduce isatoic anhydride as a sensitive and commodious fluorescent prelabel for detection of proteins in one-dimensional polyacrylamide gels. High reactivity of isatoic anhydride with nucleophiles in mild alkaline environments makes it an appropriate tag for labeling of biomolecules. In this study, we show that preelectrophoresis labeling of proteins with isatoic anhydride for few minutes at room temperature allows detection of 2-4 ng of standard proteins, BSA and lysozyme, per band. Proteins were successfully labeled in the presence of a wide range of common biological reagents and in crude cell extract. The labeled proteins have the same electrophoretic migration in comparison to unlabeled proteins; however the application of saturation labeling method results in slight band broadening. Compatibility of the method with downstream processes was assessed by tryptic digestion of labeled proteins and study of peptide mixture using gel electrophoresis which revealed partial digestion of labeled proteins due to lysine modification. The present procedure is sensitive, rapid, and inexpensive and is a promising alternative for current protein staining procedures, where downstream processes are not desired.

Isoforms of green fluorescent protein differ from each other in solvent molecules 'trapped' inside this protein

Green fluorescent protein (GFP) has been studied quite thoroughly, however, up to now some experimental data have not been explained explicitly. For example, under native conditions this protein can have two isoforms differing in their mobility in gel. In this case, no differences between the isoforms are revealed under denaturing conditions. In order to understand the difference in the isoforms of this protein, we have investigated GFP-cycle3 using mass spectrometry, gel electrophoresis, size exclusion chromatography, microcalorimetry, and spectroscopy methods under varying conditions. We have also designed and studied three mutant forms of this protein with substitutions of amino acid residues inside the GFP barrel. The mutations have allowed us to influence the formation of different GFP isoforms. Each of the mutant proteins has predominantly only one isoform. As a result of the performed research, it can be concluded that most likely the GFP isoforms differ in the solvent molecules 'trapped' inside the GFP barrel. In their turn, these molecules have an effect on the protein charge and consequently on its mobility at electrophoresis under native conditions.

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.

Transverse urea-gradient gel electrophoresis

Monitoring the cooperative unfolding transition induced when a protein is exposed to elevated temperature or a chemical denaturant is an important strategy for characterizing the conformational properties of a globular protein. This transition may be analyzed quantitatively by a variety of spectroscopic techniques, but a simpler alternative is described in this unit: urea-gradient gel electrophoresis. The pattern produced in the resulting gel can be used to estimate both the free energy change for unfolding and the rate of the unfolding transition. In addition, the technique can help identify either covalent or conformational heterogeneity in a protein sample. Because urea-gradient gel patterns are sensitive to several parameters, including hydrodynamic volume, net charge, and conformational stability, the technique can be particularly useful for comparing two forms of a protein, e.g., a natural form and the product of recombinant bacteria.

Computational and experimental approaches assess the interactions between bovine beta-lactoglobulin and synthetic compounds of pharmacological interest

Extending a previous investigation, the ability of binding to the model calycin beta-lactoglobulin (BLG) was evaluated both in silico and in vitro for several fluorine-containing (semi-)synthetic molecules of pharmacological and pharmaceutical interest (antibiotics, vastatins, steroid drugs). Simulation procedures included molecular docking according to a Montecarlo-simulated annealing protocol and molecular dynamics; heteronuclear NMR and denaturant gradient gel electrophoresis were the selected experimental techniques. For the tested drugs, ranking of the binding affinity was consistently assessed by computation and by experiment. The affinity for BLG increased in the sequence: 5-fluorosalycilic acid<dexamethasone<<sulindac=norfloxacin<fluvastatin. The computed Ki for fluorosalycilate was in the order of 10(-4)M; accordingly, in a molecular dynamics simulation the chemical diffused out of the BLG calyx in less than 2ns, and no evidence of binding was found by NMR or electrophoresis. Conversely, the Ki for fluvastatin and norfloxacin were in the order of 10(-7) and 10(-6)M, similar to the affinity for BLG by natural ligands, such as retinoids and long-chain fatty acids. Moreover fluvastatin was found still bound to the protein after 5ns of molecular dynamics simulation. Interaction of fluvastatin and norfloxacin with BLG was made evident by changes in chemical shift and dynamic parameters in the 19F NMR spectra and in effective urea concentration and cooperativity features in denaturant gradient gel electrophoresis. Such findings prove BLG may act as a drug carrier accepting in its cavity molecules of different bulk, rigidity and hydrophobicity.

Computational and experimental approaches for assessing the interactions between the model calycin β-lactoglobulin and two antibacterial fluoroquinolones

Norfloxacin and levofloxacin, two fluoroquinolones of different bulk, rigidity and hydrophobicity taken as model ligands, were docked to one apo and two holo crystallographic structures of bovine beta-lactoglobulin (BLG) using different computational approaches. BLG is a member of the lipocalin superfamily. Lipocalins show a typical b-barrel structure encompassing an internal cavity where small hydrophobic molecules are usually bound. Our studies allowed the identification of two putative binding sites in addition to the calyx. The rigid docking approximation resulted in strong repulsive forces when the ligands were docked into the calyx of the apo form. On the contrary, hindrance was not experienced in flexible docking protocols whether on the apo or on the holo BLG forms, due to allowance for side chain rearrangement. K(i) between 10(-7) and 10(-6) M were estimated for norfloxacin at pH 7.4, smaller than 10(-5) M for levofloxacin. Spectroscopic and electrophoretic techniques experimentally validated the occurrence of an interaction between norfloxacin and BLG. Changes in chemical shift and dynamic parameters were observed between the (19)F NMR spectra of the complex and of the ligand. A K(i) (ca 10(-7) M) comparable with the docking results was estimated through a NMR relaxation titration. Stabilization against unfolding was demonstrated by denaturant gradient gel electrophoresis on the complex versus apo BLG. NMR experimental evidence points to a very loose interaction for ofloxacin, the racemic mixture containing levofloxacin. Furthermore, we were able to calculate in silico K(i)'s comparable to the published experimental values for the complexes of palmitic and retinoic acid with BLG.

Dimerization and oligomerization of the chaperone calreticulin

The chaperone calreticulin is a highly conserved eukaryotic protein mainly located in the endoplasmic reticulum. It contains a free cysteine SH group but does not form disulfide-bridged dimers under physiological conditions, indicating that the SH group may not be fully accessible in the native protein. Using PAGE, urea gradient gel electrophoresis, capillary electrophoresis and MS, we show that dimerization through the SH group can be induced by lowering the pH to 5-6, heating, or under conditions that favour partial unfolding such as urea concentrations above 2.6 m or SDS concentrations above 0.025%. Moreover, we show that calreticulin also has the ability to self-oligomerize through noncovalent interactions at urea concentrations above 2.6 m at pH below 4.6 or above pH 10, at temperatures above 40 degrees C, or in the presence of high concentrations of organic solvents (25%), conditions that favour partial unfolding or an intramolecular local conformational change that allows oligomerization, resulting in a heterogeneous mixture of oligomers consisting of up to 10 calreticulin monomers. The oligomeric calreticulin was very stable, but oligomerization was partially reversed by addition of 8 m urea or 1% SDS, and heat-induced oligomerization could be inhibited by 8 m urea or 1% SDS when present during heating. Comparison of the binding properties of monomeric and oligomeric calreticulin in solid-phase assays showed increased binding to peptides and denatured proteins when calreticulin was oligomerized. Thus, calreticulin shares the ability to self-oligomerize with other important chaperones such as GRP94 and HSP90, a property possibly associated with their chaperone activity.

Applying the increase in rate constants of cooperative proteolysis to the determination of transition curves of protein denaturation

The transition curves of soybean glycinin egg lysozyme, bovine serum albumin (BSA) denaturation under the action of increasing urea concentration were monitored by determination of the increase in rate constants of cooperative enzymatic proteolysis. The results were compared with those obtained using intrinsic fluorescence and the number of accessible tyrosine. It was shown that the determination of the changes of proteolysis rate permits to disclose conformation changes not detected by other methods.

Quantitative urea gradient gel electrophoresis for studies of dissociation and unfolding of oligomeric proteins

Urea gradient gel electrophoresis combined with quantitative image processing of stained gels was used to analyze the dissociation and unfolding of the catalytic subunit of aspartate transcarbamoylase. The subunit, composed of three identical polypeptide chains, dissociates reversibly at high urea concentrations into unfolded chains. A comparison of the complex, but reproducible, gel patterns obtained for the native subunit and for the denatured protein in 6 M urea revealed significant differences at intermediate urea concentrations due to the presence of a transient kinetic intermediate identified as a relatively compact monomer. Mass transport equations based on a three state model were used to describe the urea gradient gel electrophoresis experiments, and a numerical solution yielded estimates of the population of molecular species and kinetic constants for the unfolding and refolding reactions as well as the dissociation and reconstitution reactions.

Size is a major determinant of dissociation and denaturation behaviour of reconstituted high-density lipoproteins

Lipid-free apolipoprotein A-I (apoA-I) and A-I(Milano) (A-I(M)) were compared for their denaturation behaviour by running across transverse gradients of a chaotrope, urea, and of a ionic detergent, SDS. For both apo A-I and monomeric apoA-I(M) in the presence of increasing concentrations of urea the transition from high to low mobility had a sigmoidal course, whereas for dimeric A-I(M)/A-I(M) a non-sigmoidal shape was observed. The co-operativity of the unfolding process was lower for dimeric A-I(M)/A-I(M) than for apoA-I or for monomeric apoA-I(M). A slightly higher susceptibility to denaturation was observed for dimeric A-I(M)/A-I(M) than for monomeric apoA-I(M). A similar behaviour of A-I(M)/A-IM versus apoA-I(M) was observed in CD experiments. Large- (12.7/12.5 nm) and small- (7.8 nm) sized reconstituted high-density lipoproteins (rHDL) containing either apoA-I or A-I(M)/A-I(M) were compared with respect to their protein-lipid dissociation behaviour by subjecting them to electrophoresis in the presence of urea, of SDS and of a non-ionic detergent, Nonidet P40. A higher susceptibility to dissociation of small-sized versus large-sized rHDL, regardless of the apolipoprotein component, was observed in all three instances. Our data demonstrate that the differential plasticity of the various classes of rHDL is a function of their size; the higher stability of 12.5/12.7 nm rHDL is likely connected to the higher number of protein-lipid and lipid-lipid interactions in larger as compared with smaller rHDL.

The wild type bacterial Co(2+)/Co(2+)-phosphotriesterase shows a middle-range thermostability

The phosphotriesterase (PTE) from Pseudomonas diminuta, a metalloenzyme that catalyses the hydrolysis of organophosphorus pesticides and nerve agents, has been described as a remarkably heat-stable protein [Grimsley et al., Biochemistry 36 (1997), 14366-14374]. Because substitution of the naturally occurring zinc ions by cobalt ions was found to enhance the enzyme catalytic activity, we investigated the thermal stability of the Co(2+)/Co(2+)-PTE. This study, carried out using capillary electrophoresis under optimised conditions in the pH range 9-10 compatible with optimal enzyme activity, provided evidence for irreversible denaturation according to the Lumry-Eyring model. A temperature-induced conformational transition (T(m) approximately equal to 58 degrees C) and an early growing of aggregates were observed. Comparison of UV spectra with heat-induced inactivation data clearly demonstrated that the PTE state populated above T(m) was neither native nor active. Differential scanning calorimetry showed only an exothermic trace due to aggregation of the denatured protein at T=76 degrees C. Accordingly, the temperature-induced denaturation process of the PTE could be described by a consecutive reaction model, including formation of an intermediate with enhanced activity at T approximately equal to 45 degrees C and an inactive unfolded state populated at T approximately equal to 58 degrees C, which leads to denatured aggregates. Thus, the wild type Co(2+)/Co(2+)-PTE displays a middle-range thermostability. Hence, for decontamination purposes under extreme Earth temperatures, wild type and engineered mutants of PTE substituted with other metal cations should be evaluated.

Multiple advantages of capillary zone electrophoresis for exploring protein conformational stability

This review summarizes the work of our laboratory to explore the use of capillary zone electrophoretic (CZE) methods for the investigation of protein conformational stability. Early CZE works on protein denaturation as well as fundamental and theoretical considerations are discussed. Instrumental aspects of the CE-based approach including general and particular CE requirements are documented. Several aspects dealing with estimation of stability of enzymes (cholinesterases and organophosphate-hydrolyzing enzymes) interacting with organophosphates profusely illustrate the multiple advantages of CZE. The discrimination of parameters controlling the "good compromise" stability/plasticity for allowing functional efficiency of these enzymes is exemplified. Thermal stability, susceptibility to high electric field, alteration of stability by bound ligands and the role of associated cations in metalloenzymes have been successfully investigated.

Folding/unfolding/refolding of proteins: present methodologies in comparison with capillary zone electrophoresis

A series of techniques for monitoring protein folding/unfolding/misfolding equilibria are here assessed and compared with capillary zone electrophoresis (CZE). They include spectroscopic techniques, such as circular dichroism, intrinsic fluorescence, nuclear magnetic resonance, Fourier transform infrared and Raman spectroscopy, small-angle X-ray scattering, as well as techniques based on biological assays, such as limited proteolysis and immunochemical analysis of different conformational states. Some unusual probes, such as mass spectrometry for probing unfolding transitions, are also discussed. Size-exclusion chromatography is also evaluated in view of the fact that this technique, like all electrophoretic techniques, and unlike spectroscopic probes, which can only see an average signal in mixed populations, can indeed physically separate folded vs. unfolded macromolecules, especially in the case of slow equilibria. Particular emphasis is devoted to electrophoretic techniques, such as gel-slab electrophoresis in transverse urea or thermal gradients, and CZE. In the latter case, a number of applications are shown, demonstrating the excellent correlation of CZE with more traditional probes, such as intrinsic fluorescence monitoring. It is additionally shown that CZE can be used for measuring the deltaG degrees of unfolding over the pH scale, in good agreement with theoretical calculations on the electrostatic free energy of folding vs. pH, as calculated with a linearized Poisson-Boltzmann equation. Finally, it is demonstrated that CZE can probe also aggregate formation in the presence of helix-inducing agents, such as trifluorethanol.

Interactions between carbonic anhydrase and its inhibitors revealed by gel electrophoresis and circular dichroism

Structural properties, and especially the differential stability, of complexes between carbonic anhydrase (CA) and three sulfonamide inhibitors, acetazolamide, dorzolamide and methazolamide, were investigated by spectroscopic and electrophoretic techniques. These included denaturant gradient gel electrophoresis either across a urea or a steady-state transverse sodium dodecyl sulfate (SDS) gradient. Acetazolamide, the smallest and most hydrophilic of the sulfonamides, forms the most stable complex in the presence of urea, whereas dorzolamide, with a bulky and hydrophobic structure, is most stable against the effects of SDS. At pH 7.4, complexes with dorzolamide show minimal changes in mobility across the SDS gradient, as if unaffected by the detergent, both in the presence and in the absence of excess ligand in the gel. When bound to both acetazolamide and methazolamide, on the other hand, CA displays an increase in mobility above 0.05% SDS, lower in the presence than in the absence of excess ligand. The finding of a distinct pattern for the unliganded enzyme, however, suggests the complexes can still retain the ligand, although binding of the surfactant changes their charge density. Under saturating conditions and in the presence of SDS, the surface charge of all complexes is much lower than for unliganded, denatured CA. Circular dichroism (CD) spectra clearly indicate that the increase in secondary structure and the decrease in tertiary structure brought about in CA by the presence of low concentrations of SDS are largely prevented by complexing with the inhibitors. These observations point out peculiar properties of each CA inhibitor, of potential value in the definition of their biological activities and also in the potential development of novel antagonist molecules.

Identifying and characterizing a second structural domain of protein disulfide isomerase

Recent protein engineering studies have confirmed the multidomain nature of protein disulfide isomerase previously suggested on the basis of analysis of its amino acid sequence. The boundaries of three domains, denoted a, a' and b, have been determined, and each domain has been expressed as an individual soluble folded protein. In this report, the boundaries of the final structural domain, b', are defined by a combination of restricted proteolysis and protein engineering approaches to complete our understanding of the domain organization of PDI. Using these data an optimized polypeptide construct has been prepared and characterized with a view to further structural and functional studies.

Characterization of the major bovine brain Go alpha isoforms. Mapping the structural differences between the alpha subunit isoforms identifies a variable region of the protein involved in receptor interactions

Go is the major G protein in bovine brain, with at least three isoforms, GoA, GoB, and GoC. Whereas alphaoA and alphaoB arise from a single Goalpha gene as alternatively spliced mRNAs, alphaoA and alphaoC are thought to differ by covalent modification. To test the hypothesis that alphaoA and alphaoC have different N-terminal lipid modifications, proteolytic fragments of alphao isoforms were immunoprecipitated with an N terminus-specific antibody and analyzed by matrix-assisted laser desorption ionization mass spectrometry. The major masses observed in immunoprecipitates were the same for all three alphao isoforms and corresponded to the predicted mass of a myristoylated N-terminal fragment. Structural differences between alphaoA and alphaoC were also compared before and after limited tryptic proteolysis using SDS-polyacrylamide gel electrophoresis containing 6 M urea. Based upon the alphao subunit fragments produced under activating and nonactivating conditions, differences between alphaoA and alphaoC were localized to a C-terminal fragment of the protein. This region, involved in receptor and effector interactions, implies divergent signaling roles for these two alphao proteins. Finally, the structural difference between alphaoA and alphaoC is associated with a difference of at most 2 daltons based upon measurements by electrospay ionization mass spectrometry.

Electrophoresis of proteins across a transverse sodium dodecyl sulfate gradient

We describe a new protocol for denaturant gradient gel electrophoresis, namely the migration of proteins across transverse sodium dodecyl sulfate (SDS)-gradients. We show how such gradients may be reproducibly cast, and demonstrate their stability with time once an appropriate SDS reservoir is arranged at the cathode. SDS affects both size and surface charge of the molecules, and influences the secondary and tertiary structure to a variable extent, even in opposite directions. Hence, distinct, sometimes complex, denaturation patterns may be observed for different proteins.

Sequential arrangement, not transcriptional activity, determines conformational stability of nucleosomes

Gel electrophoresis in urea gradient was applied to study the unfolding effect of increasing concentrations of urea on the nucleosome structure. We showed that conformational stability of nucleosomes is determined by nucleotide sequence but not by transcriptional activity of DNA in chromatin.

Effect of pressure on the deuterium exchange reaction of alpha-lactalbumin and beta-lactoglobulin

The effect of pressure on the deuterium exchange reaction of alpha-lactalbumin (LA) and beta-lactoglobulin (LG) was investigated to determine the structural change in these proteins induced by elevated pressure. LG, one of the main components of milk whey, has been degraded selectively from other milk proteins including LA by protease treatment under high pressure (Hayashi, R., Kawamura, Y. and Kunugi, S. J. Food Sci. 1987; 52: 1107-1108). This was considered to occur because LG lost its native structure under high pressure more remarkably than LA. In the present study, the H/D exchange reaction was carried out under high pressure and the resulting structures were analysed by Fourier-transform infra-red (FTIR) and nuclear magnetic resonance (NMR) spectroscopy, after the release of elevated pressure. The wavenumber of amide I bands in the FTIR spectrum assigned to alpha-helix and beta-sheet structures of the proteins, shifted to lower regions as the H/D exchange of protons proceeded. The integral band area of the amide proton signal in low-field regions of the NMR spectrum is related to the H/D exchange of less stable protons in the protein. H/D exchanges for LA at 200 MPa and LG at 50 MPa were detectable by NMR as a decrease in the amide proton signals, but they were detected less unambiguously by FTIR. This apparent difference may be explained by reference to an intermediary unfolding stage of the protein that is generated under moderately high pressure.

Stability, activity and structure of adenylate kinase mutants

Sequence/structure relationships have been explored by site-directed mutagenesis using a structurally known adenylate kinase. In particular the effects of helix capping and nonpolar core expansion on thermodynamic stability have been analyzed. Six point mutations were produced and characterized by SDS/PAGE, native PAGE, isoelectric focussing, electrophoretic titration, enzyme kinetics, and X-ray structure analysis. Heat-denaturation experiments yielded melting temperatures Tm and melting enthalpy changes delta Hm. The heat capacity change delta Cp of the wild-type enzyme was determined by guanidine hydrochloride denaturation in conjunction with Tm and delta Hm. Using the wild-type delta Cp value, Gibbs free energy changes delta G at room temperature were calculated for all mutants. Four mutants were designed for helix capping stabilization, but only one of them showed such an effect. Because of electrostatic interference with the induced-fit motion, one mutant decreased the catalytic activity strongly. Two mutants expanded nonpolar cores causing destabilization. The mutant with the lower stability could be crystallized and subjected to an X-ray analysis at 223-pm resolution which showed the structural changes. The enzyme was stabilized by adding a -Pro-His-His tail to the C-terminal alpha-helix for nickel-chelate chromatography. This addition constitutes a helix cap. Taken together, the results demonstrate that stabilization by helix capping is difficult to achieve because the small positive effect is drowned by adverse mutational disruption. Further addition of atoms to nonpolar cores destabilized the protein, although the involved geometry changes were very small, demonstrating the importance of efficient packing.

The Z type variation of human alpha 1-antitrypsin causes a protein folding defect

Emphysema is often associated with the Z type mutation of alpha 1-antitrypsin, which causes aggregation of the molecule in the liver and consequent plasma deficiency. The aggregation appears to be due to loop-sheet polymerization, although why the mutant protein polymerizes in vivo is unclear. Here we show that, unlike wild type antitrypsin, which folds in minutes, the folding of Z type alpha 1-antitrypsin is extremely slow. Once folded, however, the native Z protein shows substantial stability towards urea and incubation at 37 degrees C. The folding defect in Z antitrypsin leads to accumulation of an intermediate and it is the intermediate rather than the native protein which has a high tendency to aggregate.

13C-n.m.r. of the cyanylated beta-lactoglobulins: evidence that Cys-121 provides the thiol group of beta-lactoglobulins A and B

The thiol groups of beta-lactoglobulins A and B have been cyanylated using [13C]KCN. The samples of [cyanato-13C]-cyanylated-beta-lactoglobulins A and B which we prepared had signals at 109.7 p.p.m. and 114.4 p.p.m. We conclude that the thiocyanate carbon having a chemical shift of 109.7 p.p.m. is in an apolar environment similar to a cyclohexane solvent, whereas the thiocyanate carbon having a chemical shift of 114.4 p.p.m. is in a polar environment similar to water. The signals with chemical shifts of 109.7 p.p.m. are assigned to the thiocyanate carbons of the native [cyanato-13C]cyanylated-beta-lactoglobulins A and B. We deduce that the signal at 114.4 p.p.m. is due to an irreversibly denatured/unfolded species produced by alkaline denaturation, which is caused by intramolecular thiol/disulphide exchange occurring during our cyanylation procedure. We propose that Cys-119 is cyanylated in the irreversibly denatured species and Cys-121 is cyanylated in the native [cyanato-13C]cyanylated-beta-lactoglobulins A and B. We suggest that the same intramolecular thiol-disulphide exchange reactions occurred when McKenzie and co-workers [McKenzie, Ralston and Shaw (1972) Biochemistry 11, 4539-4547] alkylated beta-lactoglobulins with iodoacetamide. Therefore the one mol of thiol/mol of monomer in the native beta-lactoglobulins is due to the thiol of Cys-121 and is not due to an equimolar mixture of Cys-119 and Cys-121 as they suggested.

Native-like structure and self-association behavior of apolipoprotein A-I in a water/n-propanol solution

The effect of n-propanol on the secondary and tertiary structure of human apolipoprotein A-I (apoA-I), an interfacial protein, was investigated using near and far ultraviolet (UV)-circular dichroism (CD) and fluorescence spectroscopy, as well as limited proteolytic digestion with trypsin, and cross-linking with bis(sulfosuccinimidyl) suberate. The structure of apoA-I in n-propanol (30%, v/v) was compared with that in Tris buffer and in reconstituted, spherical or discoidal, high density lipoproteins (rHDL). Addition of n-propanol to apoA-I in Tris buffer induces major changes in its near and far CD spectra: alpha-helical content increases by 27% and the near UV-CD spectrum becomes very similar to that of apoA-I in rHDL particles. Fluorescence spectral, lifetime, and polarization results, and quenching by KI confirm that major structural changes occur in the N-terminal half of apoA-I as n-propanol is added: the Trp residues become more exposed to solvent than in buffer alone or in rHDL. Higher concentrations of guanidine hydrochloride or urea are required to denature apoA-I in n-propanol than in buffer alone, but a similar free energy of unfolding is observed. The N-terminus of apoA-I is relatively resistant to trypsin digestion and the C-terminus has equivalent digestion sites for apoA-I in the three states, but the kinetics of digestion are much slower in n-propanol and in rHDL compared to apoA-I in Tris buffer. Cross-linking experiments reveal that dimers of apoA-I exist in n-propanol, in contrast to dimers plus multimeric aggregates in Tris buffer. From these results we conclude that in 30% n-propanol the structure of apoA-I approaches that of 'native' lipid-bound apoA-I, in contrast to its structure in the aqueous Tris buffer.

Effect of pH and denaturants on the folding and stability of murine interleukin-6

The conformation and stability of a recombinant mouse interleukin-6 (mIL-6) has been investigated by analytical ultracentrifugation, fluorescence spectroscopy, urea-gradient gel electrophoresis, and near- and far-ultraviolet circular dichroism. On decreasing the pH from 8.0 to 4.0, the tryptophan fluorescence of mIL-6 was quenched 40%, the midpoint of the transition occurring at pH 6.9. The change in fluorescence quantum yield was not due to unfolding of the molecule because the conformation of mIL-6, as judged by both urea-gradient gel electrophoresis and CD spectroscopy, was stable over the pH range 2.0-10.0. Sedimentation equilibrium experiments indicated that mIL-6 was monomeric, with a molecular mass of 22,500 Da over the pH range used in these physicochemical studies. Quenching of tryptophan fluorescence (20%) also occurred in the presence of 6 M guanidine hydrochloride upon going from pH 7.4 to 4.0 suggesting that an amino acid residue vicinal in the primary structure to one or both of the two tryptophan residues, Trp-36 and Trp-160, may be partially involved in the quenching of endogenous fluorescence. In this regard, similar results were obtained for a 17-residue synthetic peptide, peptide H1, which corresponds to an N-terminal region of mIL-6 (residues Val-27-Lys-43). The pH-dependent acid quenching of endogenous tryptophan fluorescence of peptide H1 was 30% in the random coil conformation and 60% in the presence of alpha-helix-promoting solvents. Replacement of His-33 with Ala-33 in peptide H1 alleviated a significant portion of the pH-dependent quenching of fluorescence suggesting that the interaction of the imidazole ring of His-33 with the indole ring of Trp-36 is a major determinant responsible for the quenching of the endogenous protein fluorescence of mIL-6.

Unfolding of human serum transferrin in urea studied by high-performance capillary electrophoresis

High-performance capillary electrophoresis (HPCE) was used to monitor the progress of the unfolding of human serum transferrin in urea. Denaturation curves of the transferrin forms were constructed plotting the migration times corrected for the viscosity vs. the concentration of urea in the buffer. The practical advantage of capillary zone electrophoresis is the short analysis time, 5-15 min, as compared with slab-gel experiments, which require overnight runs for similar purposes. The resolution increased with the urea concentration, and hence high concentrations are beneficial for quantitative and qualitative analysis of mixtures of transferrin forms. Unfolding intermediates of the isoforms, which interconvert to the unfolded state slowly compared with the time scale of the electrophoretic separation, and also the completely unfolded isoforms were resolved and detected simultaneously when iron-free transferrin was subjected to denaturation by urea at concentrations between 3 and 6 M. However, no unfolding intermediates were observed with transferrin isoforms containing two iron atoms (i.e. diferric transferrin molecules), which accordingly are strongly resistant to urea denaturation. The unfolding of the transferrin isoforms depends on the iron content of the complexes, but not the carbohydrate content. HPCE in the presence of urea in this mode has the potential to become an analytical tool for diagnosis of diseases in which the transferrin patterns change.

Analysis of members of the Ig-gene superfamily by thermal gradient polyacrylamide gel electrophoresis

A solid aluminum block, connected with a warm and cold thermostated waterbath, provided for a linear transversal temperature gradient (TG) during polyacrylamide gel electrophoresis (PAGE). Noncovalently bound heavy chain dimers as well as heavy-light chain dimers, derived from human monoclonal IgG, could be melted into monomers using a 40-75 degrees C TG under conditions of sodium dodecyl sulfate-PAGE. Using native PAGE, major histocompatibility complex (MHC) class I molecules, preloaded with the iodinated peptide FAPGNYPAL could be melted in a 4-40 degrees C TG to release the peptide. The method is in general applicable to thermal stability analysis of noncovalently bound hetero-oligomers if the product after melting possess different electrophoretic mobilities.

Catalytically competent human and bovine zeta-thrombin and chimeras generated from unfolded polypeptide chains

Human and bovine alpha-thrombin cleaved at the B-chain by chymotrypsin generates catalytically competent zeta-thrombins, which are comprised of two noncovalently linked fragments: a 36-(human) or 49-(bovine) residue A-chain linked by a disulfide to B-chain residues B1-148 (zeta 1-thrombin) and B-chain residues B149-259 (zeta 2-thrombin). Human and bovine D-Phe-Pro-Arg-CH2-zeta- and PhMeSO2-zeta-thrombins were prepared by reaction of the active-site histidine (H-B43) and serine (S-B205) with PPACK and PMSF, respectively. Unfolding and dissociation of the noncovalently linked polypeptide chains of either human or bovine D-Phe-Pro-Arg-CH2-zeta- and PhMeSO2-zeta-thrombins in 4.5 M guanidine-HCl and refolding upon 30-fold dilution in 50 mM sodium phosphate buffer pH 6.5, 750 mM NaCl, 0.1% PEG resulted in biphasic generation of catalytic activity. The slow phase was eliminated in the presence of the competitive inhibitor benzamidine-HCl. Unfolding and refolding mixtures of the appropriate inactive precursors generated the active chimeric thrombins bovine zeta 1-thrombin:human zeta 2-thrombin and human zeta 1-thrombin:bovine zeta 2-thrombin. Human zeta 1-thrombin and zeta 2-thrombin were isolated, and, upon recombining, the isolated fragments refolded to generate catalytically competent zeta-thrombin with an active-site content, specific activity toward Chromozym-TH, and a specificity constant (kcat/Km) for FPA release from fibrinogen that were all within 60% of those of native alpha-thrombin.(ABSTRACT TRUNCATED AT 250 WORDS)

Stability of mutant actins

Mutants of the Drosophila Act88F actin gene were transcribed and translated in vitro and their relative stabilities were examined using urea gradient gel electrophoresis. Most of the mutant actins (E334K, E364K, G366D, G368E and R372H) were as stable as the wild-type. V339I had a slight decrease in stability, and E316K was the least stable. The causes of the differences are discussed and contrasted with the behaviour of the mutants in vivo, where E316K has normal stability and V339I is the least stable.

The folding and solution conformation of penicillin G acylase

The solution conformation properties of penicillin G acylase (EC 3.5.1.11) have been characterised by near- and far-ultraviolet circular dichroism, steady-state and time-resolved fluorescence spectroscopy and differential sedimentation velocity. The enzyme (86 kDa) was found to be spherical and stable unfolding over a narrow range of urea concentrations in an apparently cooperative fashion with a mid-point of 4.5 M urea. Separation of its constituent alpha and beta peptides (23.8 kDa and 62.2 kDa, respectively) was accompanied by loss of enzyme activity and unfolding, the kinetics of unfolding being highly dependent upon urea concentration. Urea gradient gel electrophoresis showed that the separated beta peptide aggregates over a wide range of urea concentrations but that the alpha peptide refolds reversibly to a compact state. Physical studies showed that the refolded alpha peptide has a compact but asymmetric structure with more alpha helix than the native enzyme, but is more sensitive to denaturant. The latter is suggested to be due to a hydrophobic patch detected by 8-anilino-1-naphthalene sulfonic acid binding and which is normally covered by the beta peptide in the native enzyme. The results of these investigations indicate that the alpha peptide constitutes a folding domain and suggest that it plays a key role in folding of the precursor for penicillin acylase.

Protein folding

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