Thermal unfolding of helices of a C-peptide analogue of ribonuclease A in sodium dodecyl sulfate solution

The conformation of a 13-residue C-peptide analogue of ribonuclease A, suc-AET-AAAKFLRAHA-CONH2, in NaDodSO4 solutions with respect to temperature was studied with CD. The equilibrium constant of unfolding yielded a straight line in a van't Hoff plot. In 10 mM NaDodSO4, delta G mu = 120 cal/mol, delta H mu = 700 cal/mol, and delta S mu = 2.0 entropy units all on per helical residue. These values compared fairly well with the thermodynamic parameters of the uncharged helix-coil transition of (Glu)n in 0.1 M NaCl based on the theories of Zimm and Bragg and Zimm and Rice. The peptide was not unfolded at 75 degrees C completely. Even in water without surfactant it was not a "random coil."     

Helical formation of a 13-residue C-peptide analogue of ribonuclease A in sodium dodecyl sulfate solution

The conformation of a 13-residue C-peptide analogue of ribonuclease A——in surfactant solutions was studied by CD. The CD spectrum of the peptide in excess NaDodSO₄ solution was typical for a helical conformation; the spectrum appeared to be virtually independent of pH (2.5–6) and temperature (3–25°C). Analysis of the CD data indicated a helicity of about 65–70% with no α-sheet and β-turn; this corresponded to 8 or 9 residues in the helical form or slightly more than two turns of α-helix. This compares with an average of about one turn of α-helix for the C-peptide analogue in water at pH 4.7 and 7°C. The conformation of the peptide in cationic surfactant, dodecyl ammonium chloride, and nonionic surfactant, dodecyl heptaoxyethylene ether, solution resembled that in water. We concluded that the C-peptide analogue can develop a maximum helicity close to the corresponding segment in ribonuclease A in hydrophobic environment provided by the clustering of NaDodSO₄ molecules to the cationic side groups of the peptide, except that the end effects may destabilize two or three residues each at both ends of the helix. Thus, in the interior of a protein molecule this hydrophobic effect may overshadow the charged-group effect than can be explained by the helix dipole model for the helical segments on the exterior of the protein molecule.     

A topological model of the interaction between alpha-synuclein and sodium dodecyl sulfate micelles

Human alpha-synuclein is a 140-amino acid protein of unknown function abundantly expressed in the brain and found in Lewy bodies, a characteristic feature of Parkinson's disease. Alpha-synuclein is random in water under physiological conditions, but the first approximately 100 residues interact with SDS micelles or acidic phospholipid small unilamellar vesicles and adopt an ordered conformation. The rest of the molecule remains disordered in the bulk of the solution. The conformation of the N-terminal portion of the molecule in lipids was described as an extended helix [Ramakrishnan, M., Jensen, P. H., and Marsh, D. (2003) Biochemistry 42, 12919-12926], as two distinct alpha-helices interrupted by a two-residue break [Chandra, S., Chen, X., Rizo, J., Jahn, R., and Sudhof, T. C. (2003) J. Biol. Chem. 278, 15313-15318], or as a noncanonical conformation, the alpha11/3 helix [Bussell, R., Jr., and Eliezer, D. (2003) J. Mol. Biol. 329, 763-778]. We characterized the topology of the different regions of alpha-synuclein relative to the surface of SDS micelles using spin probe-induced broadening of NMR signals, (15)N relaxation measurements, and fluorescence spectroscopy. Our results support the presence of two N-terminal helices, positioned on the surface of the micelle and separated by a flexible stretch. The region of residues 61-95 of the protein also adopts a helical conformation, but it is partially embedded in the micelle. These results could shed some light on the role of the membrane on the aggregation process of alpha-synuclein.     

Interaction of the interleukin 8 protein with a sodium dodecyl sulfate micelle: A computer simulation study

Molecular simulations were carried out to study the sodium dodecyl sulfate (SDS) surfactant with the interleukin 8 (IL8) protein as a model to investigate the influence of amphiphilic molecules on proteins. Simulations for an SDS micelle with an IL8 protein show that both aggregates, which were initially separated, eventually approach each other to form a single complex. The results showed that the protein was attached to the SDS micelle by the charged positive amino acids whereas less contacts were observed for the negatively charged amino acids. Structural protein properties, such as amino acid contacts and pair correlation functions were conducted between the micelle and the protein groups and they showed greater interactions between the surfactant headgroups and the positively charged residues in the protein. Moreover, hydrogen bonds were also calculated between both structures and a greater number of bonds among the SDS headgroups and the charged positive amino acids in the protein was found.

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Graphical Abstract Attachment of the interleukin 8 protein with a sodium dodecyl sulfate (SDS) micelle is given by the charged positive amino acids as indicated by the interaction of those amino acids with the SDS headgroups.

     

Secondary structural changes of non-reduced and reduced ribonuclease A in solutions of urea, guanidine hydrochloride and sodium dodecyl sulfate

The secondary structures of ribonuclease A (RNAase A) before and after reduction of the disulfide bridges and blockage of the thiol groups with iodoacetamide were examined in solutions of urea, guanidine hydrochloride, and sodium dodecyl sulfate (SDS). The relative proportions of alpha-helix, beta-structure, and disordered structure were estimated by the curve-fitting method of circular dichroism (Chen, Y.H., Yang, J.T. and Chau, K.H. (1974) Biochemistry 13, 3350-3359). The native RNAase A, with the disulfide bridges intact, contained 19% helix and 38% beta-structure. Reduction of its disulfide bridges led to a decrease in the proportion of these structures to 9% for the alpha-helix and 17% for the beta-structure. The non-reduced RNAase A resisted unfolding in low concentrations of urea and guanidine hydrochloride. The beta-structure which remained after reduction appeared to be stable even in solutions of 6 M guanidine and 9 M urea. A considerable amount of the beta-structure in both the non-reduced and the reduced RNAase A remained unaffected by high concentrations of SDS.     

Stability of aprA-subtilisin in sodium dodecyl sulfate

The effect of sodium dodecyl sulfate (SDS) on the structure and activity of aprA-subtilisin, a secreted bacterial serine protease which is 85% homologous to subtilisin BPN', was examined. The addition of SDS resulted in the slow conversion of the subtilisin from the intact protein to the completely unfolded form of the enzyme. No intermediates between these two populations were detected. This conversion was accompanied by decreased activity, disruption of tertiary structure, a change in the mobility of the protein when subjected to SDS-polyacrylamide gel electrophoresis, and an increase in the apparent Stokes radius of the protein. After 2 h in 1% SDS at 20 degrees C, 25% of the subtilisin was still intact and active. The amount of protein existing in the unfolded form was increased by increasing the length of time in SDS, by increasing the concentration of SDS, and by increasing the temperature of the subtilisin-SDS solution. Analysis of the dependence of the rate of unfolding on SDS concentration indicated that one SDS micelle can destroy two protein molecules. The activation energy for the SDS-induced denaturation of aprA-subtilisin was 20 kcal mol-1, indicating that unfolding of the protein could be the rate-limiting step.     

A rapid determination of sodium dodecyl sulfate with methylene blue.

A rapid procedure of sodium dodecyl sulfate determination was established. The method is sensitive (0–6 μg of SDS), accurate, easy to operate and uninfluenced by the presence of protein. The method is a modification of Mukerjee's that takes advantage of water-insoluble salt formation between the detergent and methylene blue, which was extracted by chloroform. Absorbance was measured in a test-tube-push-in type spectrophotometer (Bausch and Lomb Spectronic 20) with an aqueous layer on top of the chloroform; thus evaporation of chloroform was avoided and steps for removal of the aqueous phase and transfer of chloroform to cuvettes were omitted to greatly abbreviate the whole procedure.     

Cell-free protein synthesis with sodium dodecyl sulfate and ADP

A procedure is described for increasing the amount of acid-precipitable polyphenylalanine obtained from crude S-30 extracts of E. coli MRE-600 using the poly U directed Nirenberg assay system. The method requires addition of SDS and ADP to the assay solution in addition to its normal constituents. Using this procedure, a 9- to 10-fold increase in acid-precipitable radioactivity is obtained in a 60 min assay period.     

Interaction of sodium dodecyl sulfate with human native and cross-linked hemoglobins: a transient kinetic study

The interaction of sodium dodecyl sulfate (SDS) at a concentration range (0-515 microM) below the critical micelle concentration (CMC approximately 0.83 mM) with human native and cross-linked oxyhemoglobin (oxyHb) and methemoglobin (metHb) has been investigated by optical spectroscopy and stopped-flow transient kinetic measurements. It is observed that the interaction of SDS with human native and cross-linked oxyHb shows the disappearance of the bands of oxyHb at 541 and 576 nm and the appearance at 537 nm. The resultant spectra are characteristic of low spin (Fe(3+)) hemichrome. Similarly SDS has been found to convert human native and cross-linked high spin (Fe(3+)) metHb to low spin (Fe(3+)) hemichrome. The interaction of SDS with oxyHb suggests a conformational change of the protein in the heme pocket, which may induce the binding of distal histidine to iron leading to the formation of superoxide radical. The formation of hemichrome from metHb is found to be concentration-dependent with SDS. The stopped flow transient kinetic measurements of the interaction of SDS with metHb show that at least four molecules of SDS interact with one molecule of metHb. The interaction of SDS with human cross-linked oxy and met hemoglobin shows results similar to those for human native oxy and met hemoglobin indicating that the covalent modification does not alter the interaction of SDS with cross-linked hemoglobin.     

Interaction of indole and tryptophan derivatives with sodium dodecyl sulfate micelles measured with ultraviolet absorption and fluorescence quenching

The distribution of indole and tryptophan derivatives between sodium dodecyl sulfate (SDS) micellar and aqueous phases was analyzed using conventional methods of ultraviolet (UV) absorption spectroscopy and measurement of fluorescence quenching by succinimide. On the assumption of a simple pseudo-phase equilibrium between both phases the distribution coefficient was easily obtained by the measurement of the ratioR_pv of the absorbance intensity in the peak to that in the valley of the UV spectra or the fluorescence quenching constant K_sv. The possibilities and limitations of utilizing the ratio of the collisional quenching constant estimating from theK_sv value in the micellar phase to that in the aqueous phase for a measure of the polarity of the microenvironment around the tryptophan derivatives in the SDS micelle is discussed in comparison with theR_pv values for the UV spectra. The indole ring in the derivatives in the SDS micelle is localized near or on the micelle-water interface with its imino group directed toward the aqueous phase. Thus it can serve as a feasible model for interpreting the distribution coefficients andR_pv values obtained for the various indole and tryptophan derivatives.Abbreviations UV ultraviolet - SDS sodium dodecyl sulfate - ATEE N-acetyl-l-tryptophan ethyl ester - ATA N-acetyl-l-tryptophan-amide - CMC critical micelle concentration     

Interaction of sodium dodecyl sulphate with elastin polypeptides

The interaction that occurs between polypeptidic fragments of elastin and sodium dodecyl sulphate (SDS) as a model of natural amphiphilic substances has been studied by means of thermal concerration of the elastin fragments in the presence of detergents, by solubilization of a lipophilic dye, and by means of gel permeation chromatography. It was found that elastin polypeptides interact with SDS giving mixed micelles. This finding seems to be especially relevant in the tissues, revealing enhanced degradation of elastin and accumulation of lipophilic substances (e.g. in atheromatous plaques). In such tissues, elastin polypeptides formed could interfere with the formation of the normal elastic fibre by means of their interaction with amphiphilic substances.     

Parameters of interaction of sodium dodecyl sulfate with human hemoglobin

It was shown that sodium dodecyl sulfate at concentrations not exceeding the critical micelle concentrations (0-1.9 mM) induced the conversion of oxy- and methemoglobin but not deoxyhemoglobin to hemichrome. The concentration dependences of hemichrome formation were represented as Hill plots, and the parameters of detergent binding were estimated. OxyHb in 20 mM potassium-phosphate buffer, pH 6.8, has two groups of binding sites: the first group is characterized by the Hill constant n1 = 2 and the concentration of half saturation [SDS]50 = 0.8 mM, and the second group is characterized by the Hill constant n2 = 8 and [SDS]50 = 0.9 mM. In the case of metHb one group of binding sites with the Hill constant n = 2 and half saturation concentration [SDS]50 = 0.2 mM was observed. An increase in environmental pH to 7.9 decreased the affinity of Hb for SDS. It is suggested that primary binding sites for SDS in oxyHb coincide with the anion-binding center of the Hb molecule. The interaction of the detergent with these binding sites induced a structural transition of the hemoprotein molecule. As a result of this transition, secondary binding sites were exposed. In a model system (hemin--imidazole in ethanol solution), the enthalpy of the transition of hemin from a high-spin to a low-spin state was estimated to be 47 +/- 7 kJ/mol.     

Fluorescent labeling of proteins in sodium dodecyl sulfate complexes with fluorescamine

The effects of sodium dodecyl sulfate on the fluorescent labeling of proteins were studied. Of 57 primary amine groups in bovine serum albumin, no more than 7 are titrable by fluorescamine. Fluorescamine labeling does not cause appreciable conformational changes of proteins. The extent of labeling of proteins decreases as the concentrations of sodium dodecyl sulfate increases. The fluorescence properties of labeled primary amine are only slightly affected by the polarities of the solvents. The inhibitory effects of sodium dodecyl sulfate upon labelings are interpreted as the low permeability of fluorescamine toward the highly charged envelopes of sodium dodecyl sulfate-protein micelles.     

A two-state conformational transition of the extracellular ribonuclease of Bacillus amyloliquefaciens (barnase) induced by sodium dodecyl sulfate.

Barnase, the extracellular ribonuclease of Bacillus amyloliquefaciens, is shown to undergo a reversible two-state conformational transition at 0.65 mM sodium dodecyl sulfate (SDS) AAT 37 DEGREES. The prinicipal evidence is based on the equivalence of two independent values of the SDS-barnase binding ratio; about 14 mol of SDS/mol of barnase. Both were derived from fluorometric titration data, one being based on simple conservation of SDS and the other on the use of Wyman's theory of linked functions. No SDS is bound to barnase at SDS concentrations below the transition region.     

Rocket and crossed immunoelectrophoresis of proteins solubilized with sodium dodecyl sulfate

A method for the immunoelectrophoretic analysis of both hydrophilic and hydrophobic proteins from whole-cell extracts solubilized with 2% (w/v) sodium dodecyl sulfate (SDS) is described. For rocket immunoelectrophoresis, Triton X-100 is added to the sample before electrophoresis to sequester non-protein-bound SDS, and polyethylene glycol (PEG) is added to the antibody gel to enhance precipitin formation. With the optimal ratio of Triton X-100 to PEG, the quantitative determination of 5 ng of protein is possible. The SDS-solubilized sample can also be analyzed by crossed immunoelectrophoresis using SDS-polyacrylamide gels in the first dimension and antibody-containing agarose gels in the second. The best results are obtained when intermediate gels without nonionic detergents are used and when ionic detergents are omitted from the cathodal gel. Precipitin peaks of high quality, reproducibility, and without artifacts are obtained using antibody concentrations 5- to 50-fold lower than with other crossed-immunoelectrophoresis procedures.     

A precise spectrophotometric method for measuring sodium dodecyl sulfate concentration

Sodium dodecyl sulfate (SDS) is used to denature and solubilize proteins, especially membrane and other hydrophobic proteins. A quantitative method to determine the concentration of SDS using the dye Stains-All is known. However, this method lacks the accuracy and reproducibility necessary for use with protein solutions where SDS concentration is a critical factor, so we modified this method after examining multiple parameters (solvent, pH, buffers, and light exposure). The improved method is simple to implement, robust, accurate, and (most important) precise.