Further studies of detergent-induced conformational transitions in proteins. Circular dichroism of ovalbumin, bacterial alpha-amylase, papain, and beta-lactoglobulin at various pH values

Unfolding and folding pathway of lysozyme induced by sodium dodecyl sulfate

Proteins may exhibit an unfolding or folding state in the presence of a surfactant. In the present study, the unfolding and folding pathway of hen egg white lysozyme (HEWL) induced by sodium dodecyl sulfate (SDS) is studied. The stoichiometry obtained from isothermal titration calorimetry (ITC) provides guidelines for other techniques. The fluorescence spectra and circular dichroism show that the fluorescence properties and secondary structure of proteins undergo a two-step change upon binding with SDS, in which the intensity decreases, the emission blue shifts and the helical conformation decreases at low ratios of SDS to HEWL, while all of them return to the native-like state upon the addition of SDS at higher ratios. At the end of the binding, HEWL presents a higher α-helical content but its tertiary structure is lost compared to its native state, which is namely a molten globule state. Small angle X-ray scattering (SAXS) analysis and the derived model reveal that the complexes possess a decorated core-shell structure, with the core composed of dodecyl chains and the shell consisting of SDS head groups with a protein in molten globule state. Five binding steps, including the individual details involved in the denaturation, were obtained to describe the unfolding and folding pathway of HEWL induced by SDS. The results of this study not only present details about the denaturation of protein induced by SDS and the structure of the complexes involved in each binding step, but also provide molecular insights into the mechanism of the higher helical conformation of proteins in the presence of surfactant micelles.

Quantification of protein-bound sodium dodecyl sulfate by Rhodamine B: a method for identification of kinetically stable proteins

Sodium dodecyl sulfate (SDS) bound to proteins in solution could be estimated by passing through Extracti-Gel that removes free SDS followed by specific interaction of the fluorophore Rhodamine B with protein-bound SDS. The resulting fluorescence intensity is compared with a calibration curve. Whereas globular proteins respond to binding of 1.4 mg SDS/mg protein under native conditions, "kinetically stable" proteins that are otherwise resistant to denaturation due to structural integrity show a low level of SDS binding. Analysis of the circular dichroism spectrum shows that in spite of the low level of SDS binding to kinetically stable proteins under nondenaturing conditions, the detergent generates considerable secondary structure in these proteins. Because the low level of SDS binding is a general feature of kinetically stable proteins, the protocol may fulfill one of the criteria to classify a protein as kinetically stable.

The structure of the membrane-binding 38 C-terminal residues from bovine PP3 determined by liquid- and solid-state NMR spectroscopy

The secondary structure and membrane-associated conformation of a synthetic peptide corresponding to the putative membrane-binding C-terminal 38 residues of the bovine milk component PP3 was determined using 1H NMR in methanol, CD in methanol and SDS micelles, and 15N solid-state NMR in planar phospholipid bilayers. The solution NMR and CD spectra reveal that the PP3 peptide in methanol and SDS predominantly adopts an alpha-helical conformation extending over its entire length with a potential bend around residue 19. 15N solid-state NMR of two PP3 peptides 15N-labelled at the Gly7 and Ala32 positions, respectively, and dissolved in dimyristoylphosphatidylcholine/dimyristoylphosphatidylglycerol phospholipid bilayers shows that the peptide is associated to the membrane surface with the amphipathic helix axis oriented parallel to the bilayer surface.

Antibodies to a synthetic peptide that react with flavin-containing monooxygenase (HLFMO3) in human hepatic microsomes

Flavin-containing monooxygenases (FMOs) catalyze the oxidation of a diverse array of xenobiotic compounds. The purpose of this investigation was to develop a specific immunological probe to human hepatic flavin-containing monooxygenase (HLFMO3). An oligopetide corresponding to amino acid residues 257-270 of HLFMO3 was coupled to keyhole limpet hemocyanin (KLH) through the sulfhydryl group of a cysteine residue added to the amino-terminus of the peptide. This peptide-KLH conjugate was used to generate a polyclonal antibody. The resulting immunoglobulin showed specific Western blot reactivity with HLFMO3 protein in human hepatic microsomes, the same protein that is recognized by a polyclonal antibody directed against macaque liver FMO. These findings demonstrate that an antibody directed against a synthetic peptide derived from HLFMO3 can be easily produced in large quantities and used in studies for the immunodetection and immunoquantification of HLFMO3. This is also the first antipeptide antibody directed against an FMO of any species.

Effects of physicochemical factors on the secondary structure of beta-lactoglobulin

Fourier transform infrared spectroscopy and differential scanning calorimetry were used as complementary techniques to study changes in the secondary structure of beta-lactoglobulin under various physicochemical conditions. The effects of pH (3-9), NaCl (0-2 M), and lactose, glucose and sucrose (100-500 g/l) in the temperature range 25-100 degrees C on the conformation sensitive amide I band in the i.r. spectrum of beta-lactoglobulin in D2O solution were examined. The 1692 cm-1 band in the amide I band profile had not been definitively assigned in previous studies of the i.r. spectrum of beta-lactoglobulin. The decrease in this band at ambient temperature with time or upon mild heating was attributed to slow H-D exchange, indicating that it was due to a structure buried deep within the protein. The disappearance of the 1692 cm-1 band on heating was accompanied by the appearance of two bands at 1684 and 1629 cm-1, assigned to beta-sheets. The 1692 cm-1 band was therefore attributed to a beta-type structure. beta-Lactoglobulin showed maximum thermal stability at pH 3 and was easily denatured at pH 9. On denaturation, the protein unfolded into more extensive random coil structures at pH 9 than at pH 3. After 10 h at pH 9 (25 degrees C), beta-lactoglobulin was partly denatured. Heating to 60-80 degrees C generally resulted in the loss of secondary structure. At all pH values studied, two new bands at 1618 and 1684 cm-1, characteristic of intermolecular beta-sheet structure and associated with aggregation, were observed after the initial denaturation. Differential scanning calorimetry studies indicated that the thermal stability of beta-lactoglobulin was enhanced in the presence of sugars. The Fourier transform i.r. results obtained provide evidence that sugars promoted the unfolding of beta-lactoglobulin via multiple transition pathways leading to a transition state resisting aggregation.

Structural and binding characteristics of the carboxyl terminal fragment of apolipophorin III from Manduca sexta

The molecular basis of the interaction of apolipophorin III (apoLp-III), an exchangeable apolipoprotein from hemolymph of the sphinx moth. Manduca sexta, with lipoprotein surfaces and phospholipids was studied by investigating the structural and binding properties of the C-terminal fragment of the native protein. A 4K peptide, corresponding to the terminal helical segment of the native protein, was generated by cyanogen bromide treatment, purified by gel filtration and reverse-phase HPLC, and characterized by N-terminal sequencing and amino acid and mass spectrometric analysis. Circular dichroism (CD) spectroscopy of the peptide in buffer indicated a predominantly unstructured state while addition of trifluoroethanol (TFE), a helix-inducing agent, resulted in an alpha-helical structure. Sedimentation equilibrium studies revealed that the 4K peptide was monomeric in buffer. The 4K peptide assumed an alpha-helical conformation in the presence of sodium dodecyl sulfate (SDS) and lysolecithin, but was unstructured in the presence of dimyristoylphosphatidylcholine, either when added to preformed vesicles or upon cosonication, indicating an ability to bind to detergent micelles but not to phospholipid bilayers. Unlike native apoLp-III, the 4K peptide did not confer protection against turbidity development to human low density lipoprotein upon incubation with phospholipase C, indicating an inability to interact with the surface of lipoproteins. Upon interaction with SDS micelles, both the 4K peptide and apoLp-III were resistant to urea-induced denaturation when compared to free apoLp-III, as evaluated by CD spectroscopy. The structural stability conferred upon interaction with detergents was similar for both the peptide and the native protein.(ABSTRACT TRUNCATED AT 250 WORDS)

Microenvironment of tryptophan residues in beta-lactoglobulin derivative polypeptide-sodium dodecyl sulfate complexes

The changes of microenvironment of tryptophan residues in beta-lactoglobulin A and its cyanogen bromide (CNBr) fragments with the binding of sodium dodecyl sulfate (SDS) were studied with measurements of the rates of N-bromosuccinimide (NBS) modification reactions by stopped-flow photometry. Two tryptophan residues of carboxyamidomethylated (RCM) beta-lactoglobulin A in the states of their complexes with SDS were clearly distinguishable by their differences in NBS modification rates. We confirmed by experiments with CNBr fragments containing trytophan residue. The modification rates of Trp 19 in RCM beta-lactoglobulin A-SDS complexes were about 10-fold smaller than those expected for tryptophan residues exposed entirely to the aqueous solvent. The Trp 61 was hardly changed. The change of rate constants for Trp 19 was virtually consistent with those observed when N-acetyl-L-trytophan ethylester was dissolved in SDS micelles. For various species of polypeptide-SDS complexes, all tryptophan residues were reactive to NBS and also, for some of them, the differences in NBS modification rates were observed between tryptophan residues on a common polypeptide chain. These results suggest micellar and heterogeneous bindings of SDS to polypeptides.

Circular dichroism of cysteine proteinases from papaya latex. Evidence of differences in the folding of their polypeptide chains

Two forms of proteinase omega were isolated from a commercial preparation of chymopapain (EC 3.4.22.6) by means of cation-exchange liquid chromatography. Their circular dichroism (CD) spectra in the 182-320 nm region indicated that the two forms possess closely related structures. For comparison, we also recorded the CD spectra of chromatographically purified samples of papain (EC 3.422.2) and the most abundant form of chymopapain. According to the qualitative criteria proposed by Manavalan and Johnson (1983) Nature 305, 831-832), the spectral characteristics of papain correctly indicate that this protein belongs to the alpha + beta class. Proteinase omega is also placed in the alpha + beta category, while chymopapain seems to be an alpha/beta protein. Quantitative estimation of secondary structures yielded contents of helices and parallel beta-sheet that were higher in the case of chymopapain. Thus, the results of this work suggest that there are some differences in the folding pattern of chymopapain with respect to the other two proteinases. This proposal seems unexpected when the high amino acid sequence identity among these enzymes is considered.

Solution conformation of salmon calcitonin in sodium dodecyl sulfate micelles as determined by two-dimensional NMR and distance geometry calculations

The 32 amino acid hormone salmon calcitonin was studied at pH 3.7 and 7.4 by two-dimensional NMR in sodium dodecyl sulfate (SDS) micelles at 310 K. The spectrum was fully assigned, and the secondary structure was obtained from nuclear Overhauser enhancement spectroscopy (NOESY), 3JHN alpha coupling constants, and slowly exchanging amide data. Three-dimensional structures consistent with NMR data were generated by using distance geometry calculations. A set of 260 interproton distances, derived from NOESY, and hydrogen-bond constraints, obtained from analysis of the amide exchange, were used. From the initial random conformations, 13 distance geometry structures with minimal violations were selected for further refinement with restrained energy minimization. In SDS, at both pHs, the main conformational feature of the hormone is an alpha-helix from Thr6 through Tyr22, thus including the amphipathic 8-22 segment and two residues of the Cys1-Cys7 N-terminal loop. The C-terminal decapeptide forms a loop folded back toward the helix. The biological significance of this conformation is discussed.

Circular dichroic study of conformational changes in ovalbumin induced by modification of sulfhydryl groups and disulfide reduction

Sulfhydryl groups of ovalbumin were chemically modified under denaturing conditions in the absence and presence of dithiothreitol, and effects on the secondary structure of the protein were investigated by circular dichroic (CD) measurements. The contents of alpha-helix, beta-structure, and "random coil" (unordered, nonrepetitive structure) were estimated by simulation of the CD spectra and using the parameters established by Chen et al. The principal findings were these: (1) Modification of the four free sulfhydryl groups [with 5,5'-dithiobis(2-nitrobenzoic acid), iodoacetate, or iodoacetamide] caused ovalbumin molecule to unfold partially and to undergo primarily helix-to-beta structure transition. (2) Cleavage of the disulfide bond did not lead to a further conformational change in the sulfhydryl-modified ovalbumin. (3) The remaining helical structure existed in a destabilized state with increased chain flexibility, as the modified protein was very susceptible to denaturation by guanidine and urea. (4) Further evidence for increased chain flexibility was provided by the finding that sodium dodecyl sulfate (SDS) induced helix formation in the sulfhydryl-modified, but not native, ovalbumin. And (5), since both nonreduced and reduced proteins, with their sulfhydryl groups blocked, displayed similar transitions in solutions of guanidine, urea, and SDS suggested that the single disulfide bond did not physically constrain the ovalbumin molecule.

Structural similarity of chymopapain forms as indicated by circular dichroism

Four chymopapain forms were isolated by high-resolution liquid chromatography on a cation-exchange column. The three major forms possess nearly identical secondary and tertiary structures, as judged from their c.d. spectra; these components showed similar proteolytic activity and Mr values close to that of papain. The fourth isolated component seems to be a mixture of modified proteins.

Antibodies to a synthetic peptide that react specifically with a common surface region on two hydrocarbon-inducible isoenzymes of cytochrome P-450 in the rat

An antibody that reacts with two hydrocarbon-inducible isoenzymes of rat cytochrome P-450 (c and d) in the rat was produced by immunising with a synthetic peptide, Leu-Ile-Ser-Lys-Phe-Gln-Lys-Leu-Met, which has the same primary structure as that of a region of both of these isoenzymes. There was no crossreactivity with hydrocarbon-inducible isoenzymes in liver microsomes from rabbit, mouse or in man. Nor was there any crossreactivity detected with liver microsomes from uninduced rats, or rats induced with phenobarbitone or isonicotinic acid hydrazide. This is consistent with the primary structure of these isoenzymes in the regions aligned with amino acids 174-182 (the immunising peptide) in rat isoenzyme c and demonstrates the ability to produce antibodies of defined specificity against isoenzymes of cytochrome P-450 by using synthetic peptide. As the antibody preparation is able to bind to isoenzymes c and d in their native conformations, either as partially purified enzymes, or in microsomes, it is suggested that this region is present on the surface of these cytochromes P-450.

Detection and characterization by circular dichroism of a stable intermediate state formed in the thermal unfolding of papain

The thermal unfolding of papain was studied at pH 2.6 by means of circular dichroism and difference spectroscopy. The transition curves obtained from ellipticity changes at 208 and 220 nm were biphasic, i.e., they showed two distinct successive steps, demonstrating the existence of an intermediate state of stable secondary conformation in the denaturation process. Difference-spectroscopy studies indicated that considerable exposure of aromatic side-chains is involved in both steps of the transition. Since papain has two domains in its molecular structure, our results suggest that they unfold in a successive way and rather independently. Furthermore, the structural characteristics of the intermediate state, obtained from its circular dichroism spectrum in the far-ultraviolet region, seem to point out that the second domain (residues 111-212) is the most stable part of the molecule.

Binding of p-nitrophenyl phosphate and other aromatic compounds by beta-lactoglobulin

Results obtained from gel filtration showed that beta-lactoglobulin binds p-nitrophenyl phosphate with a stoichiometry of 1 mol of ligand per 18,360 monomer. Circular dichroic spectra confirmed the binding and implicated tryptophan and phenylalanine residues in the interaction. Fluorescence of the protein was quenched on binding also supporting complex formation; analysis of these data indicates that p-nitrophenyl phosphate binds to beta-lactoglobulin A with a dissociation constant of 31 microM. The B and C genetic variants of beta-lactoglobulin bind p-nitrophenyl phosphate with dissociation constants of 63 and 70 microM, respectively. In addition, a series of other nitrophenyl compounds and pyridoxal phosphate were also investigated by fluorescence analysis and found to bind to the protein. These results are discussed with respect to a recent hypothesis that beta-lactoglobulin binds retinol and is structurally related to serum retinol binding protein.

Investigations on the insertion of the mitochondrial precursor protein apocytochrome c into model membranes

Different aspects of the interaction of apocytochrome c and model membranes composed of negatively charged lipids, were studied in order to get insight into the nature of this interaction. The effect of the protein on the lipid packing properties are revealed by DSC, ESR and monolayer techniques. These experiments clearly demonstrate that upon electrostatic interaction with the negatively charged phospholipids, apocytochrome c is able to penetrate into the hydrophobic region of the model membrane. In the case of 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol, this results in a perturbation of 160 lipid molecules per apocytochrome c molecule. Most likely, apocytochrome c disrupts the formation of the gel phase and restricts the lipid chain motion above the gel to liquid-crystalline phase transition. Tryptophan fluorescence measurements confirm that at least a part of the protein penetrates into the bilayer, and suggest that after this penetration, the tryptophan (residue no. 59) is located in the glycerol backbone region of the phospholipids. Although the secondary structure of apocytochrome c is predicted to contain about 35% of alpha-helical structure, the CD pattern of an aqueous solution of the protein is featureless. However, negatively charged lipids are able to express this alpha-helical potency in the apocytochrome c, which might be important for the insertion of the protein into lipid membranes.

Anomalous behavior of bovine alpha s1- and beta-caseins on gel electrophoresis in sodium dodecyl sulfate buffers

Electrophoresis in the presence of sodium dodecyl sulfate (SDS) provides a relatively simple means of determining molecular weights of proteins. This technique relies on the validity of a correlation between some function of Mr and the mobility of the protein through the gel matrix. However, bovine caseins (especially alpha s1-casein) have lower mobilities than expected on the basis of their known Mr. The binding of SDS to both alpha s1-casein (Mr 23,600) and beta-casein (Mr 24,000) reached a maximum at the slightly low value of 1.3 g SDS/g protein. Gel-filtration chromatography showed, however, that the alpha s1-casein:SDS complex was larger than the beta-casein:SDS complex at pH 6.8 or 7.0, but that they were similar in size at pH 2.9 or 3.0. Circular dichroism spectra indicated that the low helical structure content of both alpha s1- and beta-casein increased with the addition of SDS and/or decreasing the pH to 1.5. 13C NMR results showed that SDS bound to alpha s1- and beta-casein in the same way as it did to bovine serum albumin. Either esterification or dephosphorylation followed by amidation of alpha s1-casein increased its mobility in SDS-gel electrophoresis, but neither modification affected beta-casein mobility. These and other results indicate that the low electrophoretic velocity of alpha s1-casein in SDS-gel electrophoresis results from its unexpectedly large hydrodynamic size. This is caused by localized high negative charges on certain segments of alpha s1-casein, which would induce a considerable amount of inter- and intrasegmental electrostatic repulsion, leading to an expanded or extended structure for portions of the alpha s1-casein molecule in the presence of SDS. It is clear that the conformation, and hence the equivalent radius, of an SDS:protein complex is determined by the sequence of amino acids in the protein and that, a priori, it cannot be anticipated that the electrophoretic mobility of such a complex will bear more than a casual relationship to the Mr of the protein.

Secondary structure of bovine beta-lactoglobulin B

Secondary-structure-prediction algorithms have been used to find the segments of beta-lactoglobulin sequence most likely to fit the circular dichroism assignment of 15% alpha-helix, 50% beta-sheet, and 15-20% reverse turn. A number of segments may have an alpha-helical conformation but the most prominent region of alpha-helix is from residue 129 to 143. A further probable alpha-helix segment is residues 65-76. The number of residues predicted to occur in segments of beta-sheet structure is less than expected. However, the most likely segments are for residues 1-6, 11-16, 39-45, 80-85, 92-96, 101-107, 117-123, and 145-151. Predicted reverse-turn tetrapeptides are residues 7-10, 49-52, 61-64, 88-91, and 112-115. These predicted secondary structures are consistent with the low-resolution structure of the molecule determined by X-ray diffraction studies.

Conformational study of purified epoxide hydrolase from rat liver

Hepatic epoxide hydrolase (EC 3.3.2.3) was purified from phenobarbital-treated rats by ion-exchange chromatography followed by hydrophobic chromatography. The enzyme had a specific activity of 300--400 nmol min-1 mg-1 protein with benzo[a]pyrene-4,5-oxide as the substrate. Circular dichroism (CD) spectra of the purified enzyme gave two negative bands, centered at 210 nm and 222 nm, respectively. The mean residue ellipticity at 222 nm was 12,9000 deg X cm(2) X dmol(-1), which indicated the presence of about 35% alpha-helical structures. Sodium dodecyl sulfate (SDS) greatly affected the shape of the CD spectra, which were gradually shifted to the blue. This suggested a decrease in the aggregation state of the protein. Electrostatic interactions were important in the organization of the enzyme structure since the conformation was stable between pH 7.4 and pH 10. At pH-values 5.0, 6.0 and 12.0, the CD bands underwent considerable changes in both amplitude and shape. Moreover there was a good correlation between the optimal pH range of the epoxide hydrolase activity and the organization state of the protein. After membrane reconstitution with liposomes, the conformation of the enzyme was not significantly modified by the presence of dimyristoyl L-alpha-phosphatidylcholine or other phospholipids. This constancy was obtained over a wide range of molar ratios of phospholipids to protein (0--500). However, phospholipids did increase the thermal stability of the enzyme. Fluorescence measurements of diphenylhexatriene (DPH) bound to dimyristoyl L-alpha-phosphatidylcholine indicated that addition of epoxide hydrolase modified the thermal transition of the lipid phase. On the other hand, electron paramagnetic resonance (EPR) signals of the nitroxide-labelled fatty acid, 2-(14-carboxy-tetradecyl)-2-ethyl-4,4-dimethyl-3,3,-oxazolidiny-oxyl, bound to the phospholipid, indicated that the presence of the protein decreased by about 53% the correlation time of the label, suggesting that its motion had increased. In conclusion, phospholipid-epoxide hydrolase interactions enhanced the fluidity of dimyristoyl L-alpha-phosphatidylcholine liposomes without changing the secondary structure of the enzyme. Electrostatic interactions also played an important role in the conformational stability of the protein.

Effect of various denaturing treatments on the structure and activity of a purified CP1 complex

Spinach CP1 complex, purified as previously described [16], was submitted to various dissociating treatments. Chaotropic agents, like urea and thiocyanate salts, remained without effect on the structure and photooxidation of the complex, just SDS at very high concentrations was able to dissociate the chlorophyll from the polypeptides and to abolish the photoreaction. Proteolytic enzymes have no more action on the apparent structure and activity of CP1, but some of them do cleave the large polypeptides (65 kD) into smaller ones, as observed after pigments dissociation. This last result might be an important step in the search for a smaller active P700 protein complex.

Effect of long-chain alkyl sulfate binding on circular dichroism and conformation of soybean trypsin inhibitor

The disorganization and helix formation process of "Kunitz" soybean trypsin inhibitor (STI) effected by sodium dodecyl sulfate binding was investigated by the circular dichroism (CD) probe. The binding isotherms of dodecyl sulfate to STI were determined at the ionic strength of 0.033, 0.12, and 0.25 at pH 7.3, 25 degrees C. The perturbation and disorganization of this nonhelical protein were observed at an early binding stage (v, the average molar ratio of bound detergent to STI, up to about 7 in the case of the isotherm at I = 0.12). The disappearance of a positive CD peak at 226 nm and appearance of a negative CD band at 239 nm took place at this step and were affected by the number of carbon atoms in the alkyl group of detergents. The transition of the polypeptide backbone into a more ordered conformation proceeded gradually during cooperative binding of dodecyl sulfate molecules. An abrupt increase of detergent binding occurred near the critical micelle concentration of the detergent. The helix formation was completed prior to this step (v =30, at I = 0.12).

Characterization of porins from the outer membrane of Salmonella typhimurium. 2. Physical properties of the functional oligomeric aggregates

We have purified to homogeneity, from mutant strains of Salmonella typhimurium, the small oligomers of porin that confer permeability channels to artificial vesicle membranes reconstituted from phospholipids and lipopolysaccharide. The molecular weights of the porin oligomers from the strains SH5551 and SH6017 appeared to be 130000 and 125000, respectively, and those of the monomers were 41000 and 37500, respectively, when determined by sedimentation equilibrium in the presence of dodecylsulfate. It was thus concluded that the functional porin oligomers consisted of three identical subunits. The Stokes' radius of the trimer . dodecylsulfate complex was around 5 nm. The trimer bound less dodecylsulfate than the monomer. The trimer . dodecylsulfate complex retained at room temperature the native conformation of porin, which is rich in beta-structure. When the trimers were dissociated further by various treatments, only the porin monomers were recovered in significant amounts, and the permeability-conferring activity was lost simultaneously. We propose, therefore, that the trimer is the minimal functional unit of porin that is capable of forming permeability channels in the outer membrane of Salmonella typhimurium.