Structural studies of apolipoprotein B: physical properties of the protein in guanidine hydrochloride

Apolipoprotein B was isolated from human plasma low-density-lipoprotein without precipitation by diethyl ether/ethanol extraction of the protein in 6 M guanidine hydrochloride. The physical properties of this protein, which contained a residuum of approximately 7% phospholipid, were examined in 6 M guanidine solution under reducing conditions. The circular dichroism spectrum was indistinguishable from that of a random coil protein. Sedimentation equilibrium analyses of apolipoprotein B by the meniscus depletion method of Yphantis (1984, Biochemistry 3, 297-317) were complicated by heterogeneity and nonideality despite the low concentrations employed. 63 analyses of the weight average (Mw) and z average (Mz) molecular weight were made on the apolipoprotein B from 12 subjects. The Mw observed was a function of initial concentration, rotor speed, and a heterogeneity index (Mz/Mw). Multiple linear regression of apolipoprotein B molecular mass against these parameters suggested that an Mw of 540,000 +/- 110,000 would be observed under apparently ideal and homogeneous conditions. The sedimentation coefficient and intrinsic viscosity of the reduced protein at 25 degrees C in 6 M guanidine were 2.13 S and 116 ml/g, respectively; these values predict molecular weights of 640,000 and 250,000, respectively, if apolipoprotein B was fully denatured into a random coil. Lack of agreement between these estimates and with the sedimentation equilibrium analysis can best be explained by compactness of structure and incomplete denaturation to a random coil state. Furthermore, an irreversible temperature dependence of apolipoprotein B reduced viscosity indicated that residual structure remained in solutions of 6 M guanidine hydrochloride/20 mM dithiothreitol. Taken together, the physical data demonstrate that apolipoprotein is a single polypeptide of approximately 540 kDa, whose structure resists denaturation under conditions where most proteins exist as random coils.     

The pH dependence of the reversible unfolding of ovalbumin A1 by guanidine hydrochloride.

The pH dependence of the reversible guanidine hydrochloride denaturation of the major fraction of ovalbumin (ovalbumin A1) was studied by a viscometric method in the pH range 1-7, at 25 degrees C and at six different denaturant concentrations (1.5-2.6 M). At any denaturant concentrationa reduction in pH favoured the transition from the native to the denatured state. The latter was essentially 'structureless', as revealed by the fact that the reduced viscosity of the acid and guanidine hydrochloride denatured state of ovalbumin A1 (obtained at different denaturant concentrations in acidic solutions) was measured (at a protein concentration of 3.8 mg/ml) to be 29.2 ml/g which is identical to that found in 6 M guanidine hydrochloride wherein the protein behaves as a cross-linked random coil. A quantitative analysis of the results on the pH dependence of the equilibrium constant for the denaturation process showed that on denaturation the intrinsic pK of two carboxyl groups in ovalbumin A1 went up from 3.1 in the native state to 4.4 in the denatured state of the protein.     

A guanidine hydrochloride induced change in ribonuclease without gross unfolding

Although denaturation of ribonuclease by guanidine hydrochloride to a random coil has been considered to be a simple two-state mechanism, the time dependence of our calorimetric data indicate that a cooperative endothermic pretransition may occur near 1.25 M. guanidine hydrochloride (pH 6 and 25°C) without gross unfolding of the protein. Reexamination of other observables as a function of guanidine hydrochloride concentrations as well as activity measurements suggests the possibility of some process other than simple binding occurring in the concentration range below the onset of gross denaturation.     

The hydrodynamic and conformational properties of denatured proteins in dilute solutions

Published data on the characterization of unfolded proteins in dilute solutions in aqueous guanidine hydrochloride are analyzed to show that the data are not fit by either the random flight or wormlike chain models for linear chains. The analysis includes data on the intrinsic viscosity, root‐mean‐square radius of gyration, from small‐angle X‐ray scattering, and hydrodynamic radius, from the translational diffusion coefficient. It is concluded that residual structure consistent with that deduced from nuclear magnetic resonance on these solutions can explain the dilute solution results in a consistent manner through the presence of ring structures, which otherwise have an essentially flexible coil conformation. The ring structures could be in a state of continual flux and rearrangement. Calculation of the radius of gyration for the random‐flight model gives a similar reduction of this measure for chains joined at their endpoints, or those containing loop with two dangling ends, each one‐fourth the total length of the chain. This relative insensitivity to the details of the ring structure is taken to support the behavior observed across a range of proteins.     

Spectrophotometric titration of phenolic groups of pepsin.

The ionization of tyrosine residues in diazotized pepsin under various solvent conditions was studied. All tyrosyl residues of the protein titrated normally with a pK of 10.02 in 6 M guanidine hydrochloride solution. On the other hand, two stages in the phenolic group titration curve were observed for the inactivated protein in the absence of guanidine hydrochloride; only about 10 tyrosine residues ionized reversibly up to pH 11, above which titration was irreversible. The irreversible titration zone corresponds to the pH range 11--13 in which unfolding, leading to the random coil state, was shown to occur by circular dichroism and viscosity measurements. The number of tyrosine residues exposed in the native and alkali-denatured (pH 7.5) states of diazotized protein were also studied by solvent perturbation techniques; 10 and 12 groups are exposed in the native and denatured states, respectively.     

Viscoelastic behavior of fractionated ovine submaxillary mucins.

Solution properties of fractionated ovine submaxillary mucin (OSM) and asialo OSM (aOSM) in aqueous guanidine hydrochloride have been investigated using light scattering and rheological methods. For the first time we present viscometric evidence in both dilute and concentrated solution that the molecular structure of OSM is that of a wormlike chain. The intrinsic viscosity shows molecular weight dependence consistent with the linear extended chain conformation observed by light scattering measurements. The viscoelastic behavior of the OSM fractions in aqueous guanidine hydrochloride was further examined above the overlap concentration as a function of molecular weight and temperature. Under these solvent conditions in which the role of nonbonding intermolecular interactions is minimized, OSM shows predominantly fluid like behavior. However, high molecular weight OSM shows evidence of the existence of an entanglement network at high concentration. The frequency-dependent shear storage and loss moduli at all concentrations and molecular weights can be scaled to yield a master curve by incorporating typical viscoelastic shift parameters. The entanglement molecular weight and concentration are consistent with literature data for extended, semiflexible wormlike chains. The behavior of aOSM is similar to that of intact OSM at comparable degrees of coil overlap, indicating that the terminal sialic acid residue on the carbohydrate side chain has no effect on the rheology of concentrated OSM solutions beyond that due to an increase in the hydrodynamic volume.     

Structural characteristics of extra-membrane domains and guanidine hydrochloride-induced denaturation of photosystem 2 core antenna complexes CP43 and CP47

The structural characteristics of the extra-membrane domains and guanidine hydrochloride-induced denaturation of photosystem 2 (PS2) core antenna complexes CP43 and CP47 were investigated using fluorescence emission and circular dichroism (CD) spectra. The extra-membrane domains of CP43 and CP47 possessed a certain degree of secondary and tertiary structure and not a complete random coil conformation. The tertiary structure and the chlorophyll (Chl) a microenvironment of CP47 were more sensitive to guanidine hydrochloride (GuHCl) than that of CP43. Changes in energy transfer from β-carotene to Chl a corresponded well to changes in the tertiary structure while their correlation with changes in the secondary structure was rather poor. Unlike most of water-soluble proteins, both CP43 and CP47 are partly resistant to denaturation induced by guanidine hydrochloride (GuHCl); the denaturation of CP43 or CP47 is not a two-state process. Those features most probably reflect their character as intrinsic membrane proteins.     

Occurrence and characterization of stable intermediate state(s) in the unfolding of ovomucoid by guanidine hydrochloride

Reversible unfolding of ovomucoid by guanidine hydrochloride, as followed by viscosity and difference-spectral measurements at 25°C, pH6, occurred in two distinct steps involving at least three major conformational states, namely the native, intermediate and completely denatured states, occurring respectively in 60mm-sodium phosphate buffer, 3.5m-guanidine hydrochloride and 6m-guanidine hydrochloride. The overall native conformation of ovomucoid, as indicated by its intrinsic viscosity (5.24ml/g) and gel-filtration behaviour, differs significantly from that of a typical globular protein. Exposures of tyrosine residues in native ovomucoid measured by difference spectroscopy following perturbation with glycerol, ethylene glycol and dimethyl sulphoxide were, respectively, 0.42, 0.56 and 0.57. Of the exposed phenolic groups only one titrated normally (pK_int., 9.91, electrostatic-interaction factor, w, 0.04). Results on difference spectra, solvent perturbation, phenolic titration and intrinsic viscosity (7.4ml/g) taken together showed that, although ovomucoid in 3.5m-guanidine hydrochloride was significantly unfolded, it retained a degree of native structure, removable with 6m-guanidine hydrochloride. In the latter, all the six tyrosine residues were available for titration, and the intrinsic viscosity of ovomucoid increased to 9.4ml/g. Furthermore, the characteristic fine structures in circular-dichrosim spectra of ovomucoid, associated with the elements of native structure, were abolished in 6m-guanidine hydrochloride, suggesting that the completely denatured state is structureless and presumably behaves as a cross-linked random coil. The latter state has been shown by analysis of the results on guanidine hydrochloride-dependence of the transition, intermediatedenatured, to be less stable than the intermediate state under native conditions by about 46kJ/mol at 25°C. Attempts have been made to interpret the above results in the light of available information on the amino acid sequence of ovomucoid.     

Integrity of polypeptide chains of spectrin from human erythrocytes.

The suggestion that the high molecular weight erythrocyte membrane protein, spectrin, consists of subunits resistant to dissociation by both sodium dodecyl sulfate and 6 m guanidine hydrochloride has been reevaluated. By gel electrophoresis in dodecyl sulfate and thin-layer gel filtration in 6 m guanidine hydrochloride as well as in the much more powerful denaturant guanidine thiocyanate, and by sedimentation velocity in 6 m guanidine hydrochloride, the molecular weight emerges in the range 2–2.5 × 10⁵. Denaturation profiles as a function of guanidine hydrochloride concentration, observed by circular dichroism, reveal that the spectrin conformation is unusually labile, with a mid-point for the unfolding process at a denaturant concentration near 1 m. Complete acylation with succinic anhydride, as well as reaction with citraconic anhydride, leaves the molecular weight unchanged even in 6 m guanidine hydrochloride. The possibility of measuring molecular weights of proteins by viscosity determination in trifluoroacetic acid was explored. A calibration with a series of proteins gave a Mark-Houwink plot with high scatter, which did not result from low precision of viscosity determination or protein degradation. Evidence is adduced from infrared spectra that the scatter is due to a variable degree of protonation of the polypeptide backbone in the acid, leading to altered hydrodynamic characteristics. Within the semiquantitive limits of the method, spectrin is not further disaggregated in trifluoroacetic acid. The presence of refractory noncovalent interactions and of covalent cross-links has been variously invoked to explain an apparent microheterogeneity in spectrin preparations. The results here described appear to render the former explanation untenable.     

Conformational properties of the iso-1-cytochrome C denatured state: dependence on guanidine hydrochloride concentration

Production of seven single surface histidine variants of yeast iso-1-cytochrome c allowed measurement of the apparent pK(a), pK(a)(obs), for histidine-heme loop formation for loops of nine to 83 amino acid residues under varying denaturing conditions (2 M to 6 M guanidine hydrochloride, gdnHCl). A linear correlation between pK(a)(obs) and the log of the loop size is expected for a random coil, pK(a)(obs) proportional to k log(n), where k is a scaling factor and n is the number of monomers in the loop. For small loops of nine, 16, and 22 monomers, no dependence of pK(a)(obs) on loop size was observed at any denaturant concentration indicating effects from chain stiffness. For larger loops of 37, 56, 72, and 83 monomers, the dependence of pK(a)(obs) on log(n) was linear and the slope of that dependence decreased with increasing concentration of denaturant. The scaling factor obtained at 5 M and 6 M gdnHCl for the larger loop sizes was approximately -2.0, close to the value of -2.2 expected for a random coil with excluded volume. However, scaling factors obtained under less harsh denaturing conditions (2 M to 4.5 M gdnHCl) deviated strongly from that expected for a random coil, being in the range -3 to -4. The gdnHCl dependence of pK(a)(obs) at each loop size was also evaluated to obtain denaturant m-values. Short loops where chain stiffness dominates had similar m-values of approximately 0.25 kcal/mol M. For larger loops m-values decrease with increasing loop size indicating that less hydrophobic area is sequestered when larger loops form. It is known that the earliest events in protein folding involve the formation of simple loops. The data from these studies provide direct insight into the relative probability with which loops of different sizes will form, as well as the factors which affect loop formation.     

IR spectra of cytochrome c denatured with deuterated guanidine hydrochloride show increase in beta sheet

Attenuated total reflectance Fourier transform IR (ATR-FTIR) spectra are obtained for horse heart ferricytochrome c in solutions of 0-7M guanidine hydrochloride and deuterated guanidine hydrochloride. Substitutions of deuterium for hydrogen in both the denaturant and protein provide resolvable amide I spectra over a wide range of denaturant concentrations. Deuteration enhances the ability to measure the true protein IR spectrum in the amide I region in which the secondary structure can be deduced, because spectra in D(2)O are less prone to spectral distortion upon background denaturant subtraction than spectra in H(2)O. Other investigators studying equilibrium unfolded cytochrome c were limited to guanidine concentrations below 3.0M because of detector saturation. Detector saturation is avoided with the use of ATR-FTIR spectroscopy, allowing one to obtain protein spectra at high denaturant concentrations. Second derivative spectra of samples show reductions in alpha helix and increases in beta sheet at high denaturant concentrations, contrary to expectations of finding primarily a random coil secondary structure. Using this new technique, the protein was estimated to consist of 51% beta sheet and only 15% random coil in the presence of 6.6M deuterated guanidine hydrochloride.     

Viscometric characterization of pennisetin from pearl millet

Pennisetin, the alcohol soluble storage protein of pearl millet (Pennisetum americanum), was isolated in a homogeneous state. The intrinsic viscosity [n] of this protein was found to be in the range of 16.5-17.7 ml/g in 70% (v/v) aqueous ethanol. The [eta] changed marginally when temperature was increased from 20 to 70 degrees C and also in the presence of 10 mM NaCl. The data indicated that pennisetin was a rigid, rod shaped asymmetric hydrodynamic particle with molecular dimensions in the range of 301 x 14.4 A - 317.7 x 14.2 A. During denaturation with guanidine hydrochloride (Gdn.HCl), the intrinsic viscosity of pennisetin increased from 16 to 25ml/g with a mid point at 3.6 M of the denaturant. The native protein structure was unfolded in 6 M Gdn.HCl as shown by the exposure of aromatic amino acid residues buried in the native state and this transition was found to be reversible. The intrinsic viscosity of pennisetin in 5.9 M Gdn.HCl corresponded to Mr 25,000 which was comparable to that determined by SDS-PAGE.     

Structural stability of glycophorin. Effects of heat and guanidine . HCl

The effects of guanidine hydrochloride and high temperature on human glycophorin and sialic acid-free glycophorin were monitored by circular dichroism, viscosity, and fluorescence of 1-anilino-8-naphthalane sulfonate (ANS). The following observations were made: 1. Glycophorin and its sialic acid-free counterpart are unusually stable to both guanidine . HCl and heat. 2. CD and viscosity measurements indicate that guanidine . HCl neither causes a cooperative unfolding nor generates a random coil. 3. The ANS binding site is much more sensitive to guanidine . HCl than the ellipticity at 220 nm (theta 220). 4. The effect of temperature on CD is reversible whereas the effect of guanidine . HCl is not. 5. The carbohydrate moiety influences the viscosity, and also contributes to the changes in theta 220 when solutions of glycophorin are heated. These unusual properties indicate a complex mechanism of unfolding for this structurally stable macromolecule.     

Manifestations of native topology in the denatured state ensemble of Rhodopseudomonas palustris cytochrome c'

To provide insight into the role of local sequence in the nonrandom coil behavior of the denatured state, we have extended our measurements of histidine-heme loop formation equilibria for cytochrome c' to 6 M guanidine hydrochloride. We observe that there is some reduction in the scatter about the best fit line of loop stability versus loop size data in 6 M versus 3 M guanidine hydrochloride, but the scatter is not eliminated. The scaling exponent, ν(3), of 2.5 ± 0.2 is also similar to that found previously in 3 M guanidine hydrochloride (2.6 ± 0.3). Rates of histidine-heme loop breakage in the denatured state of cytochrome c' show that some histidine-heme loops are significantly more persistent than others at both 3 and 6 M guanidine hydrochloride. Rates of histidine-heme loop formation more closely approximate random coil behavior. This observation indicates that heterogeneity in the denatured state ensemble results mainly from contact persistence. When mapped onto the structure of cytochrome c', the histidine-heme loops with slow breakage rates coincide with chain reversals between helices 1 and 2 and between helices 2 and 3. Molecular dynamics simulations of the unfolding of cytochrome c' at 498 K show that these reverse turns persist in the unfolded state. Thus, these portions of the primary structure of cytochrome c' set up the topology of cytochrome c' in the denatured state, predisposing the protein to fold efficiently to its native structure.     

Nuclear magnetic resonance studies of the denaturation of ubiquitin.

The effects of pH, temperature and guanidine hydrochloride concentration on the structure of ubiquitin, a polypeptide which can activate adenylate cyclase and can mimic thymopoietin induced differentiation of prothymocytes, were monitored using nuclear magnetic resonance spectroscopy. This relatively small polypeptide (molecular weight of 8541) exhibits a remarkable stability towards pH and temperature changes. At 7 M guanidine hydrochloride concentration, the structure of ubiquitin is essentially a random coil.     

Rheological characterization of the galactomannan from Leucaena leucocephala seed

A water soluble galactomannan isolated from Leucaena leucocephala seeds gave an intrinsic viscosity of 3.5dl/g and viscosity average molecular mass, M(v), of 6.98×10(5)g/mol. This was in reasonably good agreement with the value of the weight average molecular mass, M(w), of 5.44±0.20×10(5)g/mol determined by GPC-MALLS coupled to RI. The onset of polymer coil overlap occurred at c*[η] of 2.1, with slope of 3.0 above and 1.3 below the point of polymer coil overlap. The shear viscosity of the polysaccharide was temperature dependent and decreased with increasing temperature. The activation energy for viscous flow of 3.0% polysaccharide concentration obtained by Arrhenius plot of zero shear viscosity as a function of temperature was 26.4kJ/mol. Both the storage modulus (G') and loss modulus (G″) showed strong dependence on frequency indicating the presence of entangled coils. The Cox-Merz plot gave close superimposition of the complex and shear viscosities.     

Measuring unfolding of proteins in the presence of denaturant using fluorescence correlation spectroscopy

IFABP is a small (15 kDa) protein consisting mostly of antiparallel beta-strands that surround a large cavity into which ligands bind. We have previously used FCS to show that the native protein, labeled with fluorescein, exhibits dynamic fluctuation with a relaxation time of 35 micros. Here we report the use of FCS to study the unfolding of the protein induced by guanidine hydrochloride. Although the application of this technique to measure diffusion coefficients and molecular dynamics is straightforward, the FCS results need to be corrected for both viscosity and refractive index changes as the guanidine hydrochloride concentration increases. We present here a detailed study of the effects of viscosity and refractive index of guanidine hydrochloride solutions to calibrate FCS data. After correction, the increase in the diffusion time of IFABP corresponds well with the unfolding transition monitored by far ultraviolet circular dichroism. We also show that the magnitude of the 35 micros phase, reflecting the conformational fluctuation in the native state, decreases sharply as the concentration of denaturant increases and the protein unfolds. Although FCS experiments indicate that the unfolded state at pH 2 is rather compact and native-like, the radius in the presence of guanidine hydrochloride falls well within the range expected for a random coil.     

Nonlocal interactions stabilize compact folding intermediates in reduced unfolded bovine pancreatic trypsin inhibitor.

To further our understanding of the protein folding process, it is desirable to examine the structural intermediates (equilibrium and kinetic) that are populated between the statistical coil state and the folded molecule. X-ray crystallography and NMR structural studies are unable to determine long-range distances in proteins under denaturing solution conditions. Nonradiative (F?rster) energy transfer, however, has been shown to be a spectroscopic ruler for the measurement of distance distributions and diffusion between selected sites in proteins under a range of different solution conditions. The distributions of distances between a donor probe at the N-terminal residue and an acceptor attached to one of the four lysine residues (15, 26, 41, 46) of reduced and unfolded (in 6 M guanidine hydrochloride and 20 mM dithiothreitol) bovine pancreatic trypsin inhibitor (BPTI) were measured as a function of temperature. Even in strong denaturant and reducing agent, BPTI does not exist as a statistical coil polypeptide. It appears that nonlocal (long-range) interactions are already beginning to "fold" the protein toward a more compact, native conformation. As the temperature is increased under these conditions, hydrophobic interactions lead to an even more compact structure consistent with the predictions of phase diagrams for globular proteins.     

Fluorescence study of guanidine hydrochloride denaturation of thymidylate synthetase

The denaturation of thymidylate synthetase by guanidine hydrochloride has been studied using both the intrinsic fluorescence of the protein, and the polarization of the 1-dimethyl aminonaphthalene 5-sulfonyl conjugate of the protein. The polarization of the conjugate shows two transitions. The first transition, complete by 2.3 M guanidine, involves swelling or elongation of the protein; the second, complete by 5.5 M guanidine, is associated with unfolding of the protein. The Stokes' shift of the intrinsic protein fluorescence reflects a transition which is complete by 5.0 M guanidine hydrochloride.     

Aqueous N1-β-phenethylbiguanide hydrochloride as a solvent for protein molecular weight determination

Phenethylbiguanide (N-(2-phenylethyl)imidodicarbonimidic diamide) hydrochloride was shown to be a potent denaturing agent, according to optical rotation measurements, which at a concentration of 1.17 m yielded the proper molecular weight of reduced-carboxymethylated hen's egg lysozyme as determined by osmotic pressure measurements. The conformation of the unfolded molecule was identical to that in 6 m guanidine hydrochloride, as was shown by intrinsic viscosity measurements. The relatively low density of the solvent, 1.06 g/ml, recommends it for use in sedimentation-equilibrium studies. It would be possible to use rotor speeds 15% lower than those required when the more commonly used solvent, 6 m guanidine hydrochloride (density ～1.14 g/ml) is used.