Secondary structure transitions and aggregation induced in dynorphin neuropeptides by the detergent sodium dodecyl sulfate

Dynorphins, endogeneous opioid neuropeptides, function as ligands to the opioid kappa receptors and also induce non-opioid effects in neurons, probably related to direct membrane interactions. We have characterized the structure transitions of dynorphins (big dynorphin, dynorphin A and dynorphin B) induced by the detergent sodium dodecyl sulfate (SDS). In SDS titrations monitored by circular dichroism, we observed secondary structure conversions of the peptides from random coil to α-helix with a highly aggregated intermediate. As determined by Fourier transform infrared spectroscopy, this intermediate exhibited β-sheet structure for dynorphin B and big dynorphin. In contrast, aggregated dynorphin A was α-helical without considerable β-sheet content. Hydrophobicity analysis indicates that the YGGFLRR motif present in all dynorphins is prone to be inserted in the membrane. Comparing big dynorphin with dynorphin A and dynorphin B, we suggest that the potent neurotoxicity of big dynorphin could be related to the combination of amino acid sequences and secondary structure propensities of dynorphin A and dynorphin B, which may generate a synergistic effect for big dynorphin membrane perturbing properties. The induced aggregated α-helix of dynorphin A is also correlated with membrane perturbations, whereas the β-sheet of dynorphin B does not correlate with membrane perturbations.     

Inactivation and unfolding of aminoacylase during denaturation in sodium dodecyl sulfate solutions

During denaturation by sodium dodecyl sulfate (SDS), aminoacylase shows a rapid decrease in activity with increasing concentration of the detergent to reach complete inactivation at 1.0 mM SDS. The denatured minus native-enzyme difference spectrum showed two negative peaks at 287 and 295 nm. With the increase of concentration of SDS, both negative peaks increased in magnitude to reach maximal values at 5.0 mM SDS. The fluorescence emission intensity of the enzyme decreased, whereas there was no red shift of emission maximum in SDS solutions of increasing concentration. In the SDS concentration regions employed in the present study, no marked changes of secondary structure of the enzyme have been observed by following the changes in far-ultraviolet CD spectra. The inactivation of this enzyme has been followed and compared with the unfolding observed during denaturation in SDS solutions. A marked inactivation is already evident at low SDS concentration before significant conformational changes can be detected by ultraviolet absorbance and fluorescence changes. The inactivation rate constants of free enzyme and substrate-enzyme complex were determined by the kinetics method of the substrate reaction in the presence of inactivator previously described by Tsou [Tsou (1988),Adv. Enzymol. Related Areas Mol. Biol. 61, 381–436]. It was found that substrate protects against inactivation and at the same SDS concentrations, the inactivation rate of the free enzyme is much higher than the unfolding rate. The above results show that the active sites of metal enzyme containing Zn²⁺ are also situated in a limited and flexible region of the enzyme molecule that is more fragile to denaturants than the protein as a whole.     

Characterization of glycation in an IgG1 by capillary electrophoresis sodium dodecyl sulfate and mass spectrometry

We report a case study of characterization of a non-enzymatically glycated IgG1 using reducing capillary electrophoresis sodium dodecyl sulfate (CE–SDS) and mass spectrometry (MS). Glycation was found to occur nonspecifically at multiple sites in both the light and heavy chains. The glycated light and heavy chains result in wider peaks eluting late in the reducing CE–SDS profile; in particular, the glycated light chain behaved as a shoulder peak detected by either ultraviolet (UV) or laser-induced fluorescence (LIF) signals. The glycated species can be enriched by boronate affinity chromatography. Analyzing the enriched samples by reversed phase high-performance liquid chromatography in line with time-of-flight MS (RP–HPLC–TOF/MS) revealed adducts of +162 and +324 Da to both the light and heavy chains, suggesting the presence of multiple glycation sites. Tryptic peptide mapping and tandem mass sequencing were used to identify two glycation sites on each of the light and heavy chains.     

A micromethod for complete removal of dodecyl sulfate from proteins by ion-pair extraction

Methods are presented for the complete removal of dodecyl sulfate from proteins. Themethods utilize the extraction of dodecyl sulfate anions as ion pairs with triethylammonium or tributylammonium cations into an organic solvent. The protein is insoluble in the organic solvent and is recovered as a precipitate. The methods are applicable to microgram as well as milligram amounts of protein. In all cases studied, the recovery of protein ranges from 70 to 100%. The recovered protein is suitable for N-terminal Edman degradation, tryptic peptide mapping, and amino acid analysis and can be renatured to regain enzymatic activity and antigenicity.     

Three-dimensional structure of the ion-chanel forming peptide trichorzianin TA VII bound to sodium dodecyl sulfate micelles

Trichorzianin TA VII, Ac⁰ U¹ A² A³ U⁴ J⁵ Q⁶ U⁷ U⁸ U⁹ S¹⁰ L¹¹ U¹² P¹³ V¹⁴ U¹⁵ I¹⁶ Q¹⁷ Q¹⁸ Fol¹⁹, is a nonadecapeptide member of the peptaibol antibiotics biosynthesized by Trichoderma soil fungi, which is characterized by a high proportion of the α,α-dialkylated amino acids, α-aminoisobutyric acid (Aib, U) and isovaline (Iva, J), an acetylated N-terminus and a C-terminal phenylalaninol (Pheol, Fol). The main interest in such peptides stems from their ability to interact with phospholipid bilayers and form voltage-dependent transmembrane channels in planar lipid bilayers. In order to provide insights into the lipid-peptide interaction promoting the voltage gating, the conformational study of TA VII in the presence of perdeuterated sodium dodecyl sulfate (SDS-d25) micelles has been carried out. ¹H sequential assignments have been performed with the use of two-dimensional homo- and -heteronuclear nmr techniques including double quantum filtered correlated spectroscopy, homonuclear Hartmann-Hahn, nuclear Overhauser effect spectroscopy, ¹H-¹³C heteronuclear single quantum correlation, and heteronuclear multiple bond correlation. Conformational parameters, such as ³ J _NHCαH coupling constants, temperature coefficients of amide protons (Δδ/Δ T _NH) and quantitative nuclear Overhauser enhancement data, lead to detailed structural information. Ninety-eight three-dimensional structures consistent with the nmr data were generated from 231 interproton distances and six Φ dihedral angle restraints, using restrained molecular dynamics and energy minimization calculations. The average rms deviation between the 98 refined structures and the energy-minimized average structure is 0.59 Å for the backbone atoms. The structure of trichorzianin TA VII associated with SDS micelles, as determined by these methods, is characterized by two right-handed helical segments involving residues 1–8 and 11–19, linked by a β-turn that leads to an angle about 90°–100° between the two helix axes; residues 18 and 19 at the end of the C-terminal helix exhibit multiple conformations. © 1998 John Wiley & Sons, Inc. Biopoly 46: 75–88, 1998     

Inactivation and dissociation of rice ribulose-1,5-bisphosphate carboxylase/oxygenase during denaturation by sodium dodecyl sulfate

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is a key enzyme in photosynthesis and photorespiration. The inactivation and subsequent conformational changes and dissociation of rice Rubisco by SDS have been studied. At low SDS concentrations (0.4 mM), Rubisco completely lost its carboxylase activity and most of its sulfhydryl groups became exposed. Dissociation of small subunits and significant conformational changes occurred at higher SDS concentrations. Increasing SDS concentrations caused only slight changes in CD spectrum, indicating no significant effect of SDS on the secondary structure of the enzyme. The results prove that the active site of Rubisco is more fragile to denaturants than the protein as a whole. The results also suggest that small subunits are more liable to SDS denaturation and thus dissociate first, while the more hydrophobic large subunits remain complexed. The naturally existing hydrophobic surface of Rubisco may be an important factor in the interaction of Rubisco with other macromolecules.     

Separation of mammalian cytochrome c oxidase into 13 polypeptides by a sodium dodecyl sulfate-gel electrophoretic procedure

A sodium dodecyl sulfate-gel electrophoretic procedure which allows the separation of isolated cytochrome c oxidase from different mammalian sources into 13 different polypeptides is described. Application of the silver-staining procedure results in the same protein pattern as obtained by Coomassie blue staining. From the correlation of the gel bands with 12 isolated polypeptides from which the complete amino acid sequence is known, it is concluded that mammalian cytochrome c oxidase consists of 13 different polypeptides which can all be separated by the described procedure.     

Studies on interaction of oligopeptides with sodium dodecyl sulfate: Stopped-flow kinetics of chemical modification of tryptophan residues withN-bromosuccinimide

The stopped-flow kinetics of the reaction between oligopeptides containing tryptophan residues andN-bromosuccinimide (NBS) were studied in 50 mM sodium phosphate buffer (pH 7.0) containing sodium dodecyl sulfate (SDS). Decreases in the reaction rates attributable to the interaction between oligopeptides and SDS were observed, and oligopeptides studied were classified into types I and II on the basis of the interaction modes. Type I oligopeptides were dissolved in SDS micelles; type II oligopeptides interacted cooperatively with SDS monomers. The manner of interaction between SDS and oligopeptides of type II could be interpreted by a simple equilibrium relation: oligopeptide+n·(SDS)=oligopeptide·(SDS) _n .     

Low sodium dodecyl sulfate concentrations inhibit tobacco mosaic virus coat protein amorphous aggregation and change the protein stability

Effects of low SDS concentrations on amorphous aggregation of tobacco mosaic virus (TMV) coat protein (CP) at 52 degrees C and on the protein structure were studied. It was found that SDS completely inhibits the TMV CP (11.5 microM) unordered aggregation at the detergent/CP molar ratio of 15 : 1 (0.005% SDS). As judged by fluorescence spectroscopy, these SDS concentrations did not prevent heating-induced disordering of the large-distance part of the TMV CP subunit, including the so-called "hydrophobic girdle". At somewhat higher SDS/protein ratio (40 : 1) the detergent completely disrupted the TMV CP hydrophobic girdle structure even at room temperature. At the same time, these low SDS concentrations (15 : 1, 40 : 1) strongly stabilized the structure of the small-distance part of the TMV CP molecule (the four alpha-helix bundle) against thermal disordering as judged by the far-UV (200-250 nm) CD spectra. Possible mechanisms of TMV CP heating-induced unordered aggregation initiation are discussed.     

Influence of heat and sodium dodecyl sulfate on the endopeptidase I from Bacillus sphaericus 9602

Endopeptidase I from Bacillus sphaericus is a stable enzyme which retains its activity at 37 degrees C in the presence of sodium dodecyl sulfate. Polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate revealed two forms of the enzyme: an active, fast-running form, for the enzyme preheated at 37 degrees C and a denatured, slow-running form, for the enzyme preheated at 100 degrees C. Such behavior is similar to that of the "heat-modifiable" outer membrane proteins from gram-negative bacteria. In the absence of sodium dodecyl sulfate, endopeptidase I aggregated in an enzymatically active dimer, with an apparent molecular weight of 90,000 daltons, which could be the native form of the enzyme.     

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.     

十二烷基硫酸钠辅助提取布渣叶中的黄酮类物质

以布渣叶为研究体系,采用表面活性剂辅助热回流法提取黄酮类物质.考察了表面活性剂种类及浓度、提取时间、液固比和溶剂pH等因素,并通过实验数据进行了正交试验设计,得到最优的工艺条件:表面活性剂选择十二烷基硫酸钠(SDS),质量浓度0.8 g/L,提取时间105 min,液固比45 mL/g,溶剂pH 6.3.在此条件下,布渣叶黄酮得率为15.73％,与其他方法相比具有显著优势.     

十二烷基硫酸钠协同微波-酶法提取布渣叶总黄酮

采用十二烷基硫酸钠(SDS)协同微波-酶法提取布渣叶总黄酮,选取微波辐射时间(X1)、SDS质量分数(X2)、液固比(X3)、恒温水浴提取时间(X4)、酶解时间(X5)进行U15(54×3)混合水平均匀试验设计,利用偏最小二乘法(PLS)处理试验数据,建立数学模型,确定提取的最优条件并进行验证;另外,将优化后的提取结果与其他提取方法进行比较.研究结果表明:优化的提取条件为X1=1min、X2=0.16％、X3=30.75 mL/g、X4=50 min、X5=30 min.与其他提取方法相比,该法提取效率高,环保无污染,具有一定的应用价值.     

Stop-flow kinetics studies of the interaction of surfactant, sodium dodecyl sulfate, with acid-denatured cytochrome c

Interactions of sodium dodecyl sulfate (SDS) at submicellar and micellar concentration, with the globular protein, horse heart cytochrome c, at low pH have been shown to stabilize two molten globule-like intermediates. These dynamic studies were performed using far-UV, near-UV, and Soret-band circular dichroism (CD) as well as fluorescence methods. Stopped-flow CD and fluorescence studies of acid-denatured cytochrome c refolding with SDS were performed at both submicellar and micellar concentrations. Distinctive refolding mechanisms (from analysis of both CD and fluorescence) were found under these two conditions, and an obvious refolding intermediate was evident in the fluorescence traces. In addition, stopped-flow CD in the Soret region showed multistep kinetics, suggesting that the spectral changes in this region are not only solvent effect related but also connected with the change of secondary structure. A possible folding mechanism is proposed to rationalize the kinetics results.     

Application of sodium dodecyl sulfate electrophoresis of hemolysate to the biochemical systematics of the rockfish Sebastes

Sodium dodecyl sulfate electrophoresis of rockfish hemolysate was carried out to investigate problems in the systematics of the genus Sebastes. Results generally revealed species-specific electropherograms that were generally intra-specifically invariant. Experimental findings supported the distinction of S. chrysomelas and S. carnatus as valid species which hitherto had not been accomplished on a morphometric or meristic basis. Moreover, common protein subunits occurred within all specimens studied, and additional interspecific differences suggested several biochemical subgroupings (caurinus, nebulosus; paucispinis, goodei; carnatus, chrysomelas, atrovirens, melanops, mystinus and serranoides). These proposed subgroupings generally differed from previous classifications based on morphometric and meristic data. Some of these differences may ultimately be attributed to pressure adaptive differences in the hemoglobin molecule.     

Protein-SV40 DNA complex stable in high salt and sodium dodecyl sulfate.

A protein-DNA complex which is stable in concentrated salt solutions and in the presence of sodium dodecyl sulfate has been extracted from purified viruses and is found in the nicked circular DNA fraction. The protein is visualized as a “dot” on the DNA molecule by electron microscopy using a modified version of the ethidium bromide mounting technique. The position of the dot is at 0.67 genome units clockwise from the ecoRI restriction site on the SV40 DNA map.     

Interaction of bradykinin with sodium dodecyl sulfate and certain acidic lipids

The striking change in the circular dichroism (CD) of bradykinin (BK) occasioned by its interaction with sodium dodecyl sulfate (SDS) is evidently due in large part to a change in the conformation of the C-terminal tetrapeptide moiety of the hormone. The full change in CD is induced by the binding of two molecules of monomeric SDS per peptide molecule, the complex being aggregated. Formation of the 1:2 BK-SDS complex apparently proceeds via intermediates of stoichiometry 1:1 and 2:1. The cooperative nature of the interaction is attributed to the SDS-promoted aggregation of BK. Electrostatic interactions with the Arg residues appear important for the binding reaction per se. CD reveals that BK also interacts with acidic lipids which bear a net electrical charge (e.g., cerebroside sulfate and phosphatidyl inositol) but not with lipids bearing no net charge (e.g., cerebroside and phosphatidyl choline). The interactions are with particular mixed micelles of the lipid and the nonionic surfactant used for their solubilization, micellar size and structure being examined by surface tensiometry and electron microscopy.     

Detection of enzymatic activities in sodium dodecyl sulfate-polyacrylamide gels: DNA polymerases as model enzymes

Recent techniques for detecting the catalytic activity of enzymes in sodium dodecyl sulfate (SDS)-polyacrylamide gels have been hampered by lack of reproducibility associated with variability in commercial SDS preparations. Simple expedients which facilitate reproducible detection of DNA polymerase activity and which appear to be widely applicable to detection of other enzymes are reported here. It was observed that reproducibility of a reported procedure for DNA polymerase detection (Spanos, A., Sedgwick, S. G., Yarranton, G. T., Hübscher, U., and Banks, G. R. (1981) Nucl. Acids Res.9, 1825–1839) depends on the SDS used for electrophoresis, and that sensitivity is markedly reduced if currently available SDS is substituted for the discontinued product specified by Spanos et al. A modified procedure yielding sensitivity with contemporary commercial SDS, which exceeds the sensitivity observed when using the protocol and the SDS originally specified, is described. The modifications employed, which presumably promote renaturation of enzymes, are (1) embedding fibrinogen in gels and (2) washing detergent from gels with aqueous isopropanol after electrophoresis. These expedients permit detection of picogram amounts of Escherichia coli DNA polymerase I and its Klenow fragment and nanogram amounts of calf thymus α and rat liver (Novikoff hepatoma) β polymerases. Finally, it is shown that sensitivity of DNA polymerase detection is reduced by lipophilic contaminants in contemporary commercial SDS, and that the expedients employed here mitigate the deleterious effect of these impurities.     

rgn gene is required for gut cell homeostasis after ingestion of sodium dodecyl sulfate in Drosophila

Resistance and resilience constitute the two complementary aspects of epithelial host defenses in Drosophila. Epithelial cell homeostasis is necessary for the recovery of damages caused by stress or infections. However, the genes responsible for gut epithelial homeostasis remain poorly understood. Here, we show that rgn^G4035 mutant flies have higher mortality than wild-type flies after ingestion of sodium dodecyl sulfate (SDS). Excessive melanization and increased necrotic cells in the gut contribute to the reduced survival of rgn^G4035 mutant flies following SDS ingestion. rgn mutant flies have a defect in the replenishment of intestinal stem cells (ISCs) following gut damage. The antimicrobial peptide (AMP) expression is affected in rgn^G4035 mutant fly guts. Together, our study provides evidence that rgn gene is essential for gut cell homeostasis following damage in Drosophila.