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PubMed1998

NMR study of the conformation and localization of porcine galanin in SDS micelles. Comparison with an inactive analog and a galanin receptor antagonist.

Galanin is a 29/30-residue neuro-endocrine peptide which performs its many important physiological functions via a membrane-bound receptor. By using two-dimensional proton NMR spectroscopy, complete relaxation matrix analysis, and simulated annealing, the conformation of porcine galanin was determined in a membrane-mimicking solvent containing sodium dodecyl sulfate (SDS) micelles. The final family of calculated structures displays three well-defined beta- or gamma-turn regions, comprising residues 1-5, 7-10, and 24-27, but has otherwise a random conformation. The receptor-interacting N-terminal part, residues 1-5, was found to be best defined with a backbone RMSD value of 0.12 A. The mode of association between galanin and the SDS micelle was determined by observing the broadening effect on proton resonances, when spin-labeled 5- and 12-doxyl stearate molecules were added. It was concluded that galanin is located close to the surface of the micelle with two regions, residues 6-9 and 24-29, as well as two single residues, 18 and 21, reaching out into the aqueous solvent. Additional NMR studies were carried out on an inactive analogue, Ala2-galanin, and an antagonist M40. The results show that the proton resonances of galanin and M40 have identical chemical shifts in the N-terminal receptor-interacting region, indicating similar solution structures in this region. For Ala2-galanin, the same region displays a spectral heterogeneity with chemical shifts clearly different from the other two peptides, indicative of different secondary structures. These results may provide a structural background for the antagonist activity of M40 and the hormonal inactivity of Ala2-galanin, as compared to galanin.

Alanine↗
PubMed2005

Tuning the structure of SDS micelles by substituted anilinium ions.

The growth behavior of aggregates formed in aqueous solutions of the anionic surfactant sodium dodecyl sulfate (SDS) in the presence of the cationic hydrophobic salts o-toluidine hydrochloride (OTHC) and m-toluidine hydrochloride (MTHC) has been studied by dynamic light scattering (DLS) and small-angle neutron scattering (SANS) techniques. DLS studies indicate a progressive growth of SDS micelles with addition of less than equimolar concentrations of hydrophobic salts. A prolate ellipsoidal model is used to analyze the DLS data, which is further supported by SANS measurements. We explain the propensity for the strong growth of micelles in the presence of OTHC and MTHC by the high charge neutralization provided by these salts as the aromatic counterions are adsorbed on the surface of the micelles. When the substitution is at the meta position, i.e., for MTHC, micellar growth is favored at lower salt concentrations than for OTHC. The variation in growth behavior is explained in terms of the difference in the chemical environments of the substituents at the ortho and meta positions. Micellar parameters obtained from SANS data at elevated temperature also support enhanced growth of micelles in the presence of MTHC as compared to OTHC.

Aniline Compounds↗
PubMed2004

Study of copper sulfide crystallization in PEO-SDS solutions.

The crystallization of copper sulfide in aqueous supersaturated solutions in the presence of the polymer poly(ethylene oxide), PEO, and the surfactant sodium dodecyl sulfate, SDS, was investigated. In these systems, copper sulfide precipitation competes with the reaction between copper cations and dodecyl sulfate anions. The competition of the two reactions may affect the reaction products significantly; therefore it is important to study the properties of the surfactant salt, copper dodecyl sulfate (Cu(DS)2), in detail. The thermodynamic solubility constant of Cu(DS)2 was measured at 8 degrees C and was equal to (2.4 +/- 0.4) x 10(-10) M3. The Krafft point of Cu(DS)2 and its solubility curve (precipitation temperature for a range of concentrations) were also measured. The latter was found to be very close to room temperature. Temperature is thus a very significant parameter in these systems and must be carefully controlled in all experiments. The crystallization of copper sulfide in PEO-SDS solutions was investigated in solutions with compositions above and below the solubility curve. Copper sulfide nanoparticles predominate and are stabilized at temperatures above the solubility curve. Surprisingly, at temperatures below the solubility curve CuxS coexists with Cu(DS)2, which appears in the form of lamellar crystals. The system is further complicated by the presence of at least two different types of copper sulfides corresponding to different oxidation states of copper. Our results suggest that the predominance of Cu(DS)2 at lower temperatures is due to its limited solubility and is modified by the CuI/CuII redox equilibrium in combination with the solution pH.

Journal Article↗
PubMedDate not supplied

Temperature-, SDS-, and pH-induced conformational changes in protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus: a dynamic simulation and fourier transform infrared spectroscopic study.

The effect of SDS, pD, and temperature on the structure and stability of the protein disulfide oxidoreductase from Pyrococcus furiosus (PfPDO) was investigated by molecular dynamic (MD) simulations and FT-IR spectroscopy. pD affects the thermostability of alpha-helices and beta-sheets differently, and 0.5% or higher SDS concentration influences the structure significantly. The experiments allowed us to detect a secondary structural reorganization at a definite temperature and pD which may correlate with a high ATPase activity of the protein. The MD simulations supported the infrared data and revealed the different behavior of the N and C terminal segments, as well as of the two active sites.

Adenosine Triphosphatases↗
PubMed2006

VDAC1, having a shorter N-terminus than VDAC2 but showing the same migration in an SDS-polyacrylamide gel, is the predominant form expressed in mitochondria of various tissues.

The voltage-dependent anion channel (VDAC) is a pore-forming protein expressed in the outer membrane of eukaryotic mitochondria. Three isoforms of it, i.e., VDAC1, VDAC2, and VDAC3, are known to be expressed in mammals; however, the question as to which is the main isoform in mitochondria is still unanswered. To address this question, we first prepared standard VDACs by using a bacterial expression system and raised various antibodies against them by using synthetic peptides as immunogens. Of the three bacterially expressed VDAC isoforms, VDAC3 showed faster migration in SDS-polyacrylamide gels than VDAC1 and VDAC2, although VDAC2 is longer than VDAC1 and VDAC3, due to a 12-amino acid extension of its N-terminal region. Even with careful structural characterization of the expressed VDACs by LC-MS/MS analysis, serious structural modifications of VDACs causing changes in their migration in SDS-polyacrylamide gels were not detected. Next, immunoreactivities of the raised antibodies toward these bacterially expressed VDAC isoforms were evaluated. Trials to prepare specific antibodies against the three individual VDAC isoforms were not successful except in the case of VDAC1. However, using a synthetic peptide corresponding to the highly conserved region among the three VDACs, we were successful in preparing an antibody showing essentially equal immunoreactivities toward all three VDACs. When mitochondrial outer membrane proteins of various rat tissues were subjected to 2-dimensional electrophoresis followed by immunoblotting with this antibody, six immunoreactive protein spots were detected. These spots were characterized by LC-MS/MS analysis, and the signal intensities among the spots were compared. As a result, the signal intensity of the spot representing VDAC1 was the highest, and thus, VDAC1 was concluded to be the most abundantly expressed of the three VDAC isoforms in mammalian mitochondria.

Amino Acid Sequence↗
PubMed2000

Structural study of the sodium channel inactivation gate peptide including an isoleucine-phenylalanine-methionine motif and its analogous peptide (phenylalanine/glutamine) in trifluoroethanol solutions and SDS micelles.

In order to gain insight into the gating mechanisms of Na+ channels, in particular their inactivation mechanisms, we studied the structures of the Na+ channel inactivation gate related peptide which includes the IFM (Ile-Phe-Met) motif (Ac-KKKFGGQDIFMTEEQKK-NH2; K1480-K1496 in rat brain type-IIA Na+ channels, MP-3A) and its F/Q(Gln) substituted one (MP-4A) in trifluoroethanol (TFE) solutions and sodium dodecyl sulfate (SDS) micelles using circular dichroism (CD) and 1H-NMR spectroscopies. Based on observed nuclear Overhauser effect constraints, three-dimensional structures of MP-3A and MP-4A were determined using simulated annealing molecular dynamics/ energy minimization calculations. In TFE solutions, no appreciable differences in the structure were observed using either CD or NMR spectra. In SDS micelles, however, the two peptides exhibited definitely different structures from each other. It was found that in MP-3A, residues 11488 and T1491 were spatially proximate with each other owing to hydrogen bonding between the amide proton of 11488 and the hydroxyl oxygen atom of T1491, whereas in MP-4A, F/Q substitution separated them owing to conformational changes. The solvent-accessible surfaces calculated for the structures of MP-3A and MP-4A showed that the former has a smoother interaction surface to the hydrophobic docking site than the latter. In conclusion, the conformational changes, as well as decreased hydrophobicity around the IFM motif owing to the F/Q mutation, may be one reason why F1489Q mutated channels cannot inactivate almost completely.

Amino Acid Motifs↗
PubMed2002

Cloning and molecular characterization of a SDS-activated tyrosinase from Marinomonas mediterranea.

The sequence of the tyrosinase gene cloned from Marinomonas mediterranea is reported. It is the second tyrosinase cloned from a Gram negative bacterium. Its size is higher than that of Gram positive tyrosinases from Streptomyces, and more similar to the eukaryotic enzymes. Its sequence shares the features of copper-binding sites found in all tyrosinases. Based in the comparison of tyrosinases from all types of organisms, an extension of the characteristic signatures existing at Prosite is proposed. This tyrosinase shares with some plant and amphibian tyrosinases a strong specific activation by submicellar concentrations of SDS. Intrinsic fluorescence and kinetic properties indicate that the activation is caused by an SDS-dependent conformational change that facilitates the substrate accessibility to the dicopper active site.

Amino Acid Sequence↗
PubMed1987

Identification of glycoproteins expressing tumour-associated PNA-binding sites in colorectal carcinomas by SDS-GEL electrophoresis and PNA-labelling.

Many tumour-specific antigens in gastrointestinal cancers have carbohydrate immuno-determinants. These epitopes can be identified by lectins and monoclonal antibodies. By using fluorescein-isothiocyanate (FITC)-conjugated peanut agglutinin (PNA) and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) we have investigated glycoproteins carrying altered carbohydrate epitopes in normal and carcinomatous human colorectal mucosa. In normal mucosa PNA stained goblet cell glycoconjugates in the supranuclear (Golgi) distribution. After neuraminidase pretreatment PNA stained actual mucin goblet itself at all levels of the crypts. Colorectal carcinomas displayed a strong and direct binding of PNA to apical cell membranes of carcinomatous cells and intraluminal secretions. Analysis of the glycoproteins by SDS-PAGE and PNA-labelling revealed four carcinoma-associated glycoproteins (26kD, 32kD, 35kD and 50kD). In addition, four glycoproteins (29kD, 30kD, 33kD and 36kD) common to normal and carcinomatous colorectal mucosa could be identified. All of these glycoproteins differed in their molecular weight from those in red cell controls which bind PNA only after desialylation. The study shows that the expression of PNA-binding sites in colorectal carcinomas signifies a cancer-associated carbohydrate alteration. Four carcinoma-associated glycoprotein antigens could be detected by this lectin. The antigens we have identified might be useful in the isolation and purification of more selective reagents for the serologic detection of colorectal cancer.

Antigens, Neoplasm↗
PubMed2002

Apolipoprotein E structural requirements for the formation of SDS-stable complexes with beta-amyloid-(1-40): the role of salt bridges.

Of the three major isoforms of human apolipoprotein E (apoE), apoE4 is a risk factor for the development of Alzheimer's disease. Among possible neurologically relevant differences in the properties of apoE3 and apoE4 is the fact that apoE3 forms an SDS-stable complex with beta-amyloid-(1-40) (Abeta40) with greater avidity than does apoE4. This interaction may sequester potentially toxic species of Abeta or facilitate clearance. To understand more about this difference, we examined whether differences in salt bridges between apoE domains influence the capacity of apoE isoforms to form complexes with Abeta. In apoE3 there is a salt bridge between Arg-61 and Asp-65, while in apoE4 there are salt bridges between Arg-61 and Glu-255, and Arg-112 and Glu-109. Mutation of position 112, which is Cys in apoE3 and Arg in apoE4, to Ala or Lys abolished complex formation, while mutant apoE with Ser at this position retained the capacity to form complex. Substituting Ala for Glu-109 had no effect on the ability of either apoE4 or apoE3 to form complexes. On the other hand, substitution of Thr for Arg-61 in apoE3 abolished, and truncation of apoE3 at position 201 substantially lowered, but did not abolish, complex formation. Neither of these mutations within apoE4 had any affect on its complex formation with Abeta. These results suggest that the nature of the cysteine residue in apoE3 and interactions between the N-terminal and C-terminal domains of human apoE are important for the ability of apoE3 to form an SDS-stable complex with Abeta40.

Alzheimer Disease↗
PubMed2006

The conformational state of polyphenol oxidase from field bean (Dolichos lablab) upon SDS and acid-pH activation.

Field bean (Dolichos lablab) contains a single isoform of PPO (polyphenol oxidase)--a type III copper protein that catalyses the o-hydroxylation of monophenols and oxidation of o-diphenols using molecular oxygen--and is a homotetramer with a molecular mass of 120 kDa. The enzyme is activated manyfold either in the presence of the anionic detergent SDS below its critical micellar concentration or on exposure to acid-pH. The enhancement of kcat upon activation is accompanied by a marked shift in the pH optimum for the oxidation of t-butyl catechol from 4.5 to 6.0, an increased sensitivity to tropolone, altered susceptibility to proteolytic degradation and decreased thermostability. The Stokes radius of the native enzyme is found to increase from 49.1+/-2 to 75.9+/-0.6 A (1 A=0.1 nm). The activation by SDS and acid-pH results in a localized conformational change that is anchored around the catalytic site of PPO that alters the microenvironment of an essential glutamic residue. Chemical modification of field bean and sweet potato PPO with 1-ethyl-3-(3-dimethylaminopropyl)carbodi-imide followed by kinetic analysis leads to the conclusion that both the enzymes possess a core carboxylate essential to activity. This enhanced catalytic efficiency of PPO, considered as an inducible defence oxidative enzyme, is vital to the physiological defence strategy adapted by plants to insect herbivory and pathogen attack.

Acids↗
PubMed1997

Fractionation of mycobacterial integral membrane proteins by continuous elution SDS-PAGE reveals the immunodominance of low molecular weight subunits for human T cells.

Integral membrane proteins (IMP) represent a serologically distinct class of mycobacterial antigens which are potent stimulators of human T cells (Mehrotra et al., Clin Exp Immunol 1995; 102:626). The range of IMP from Mycobacterium fortuitum was resolved by continuous elution SDS-PAGE to recover 31 discrete fractions covering bands up to approximately 58 kD. The fractions, after removal of SDS, were subjected to human T cell proliferation assays for the identification of immunodominant molecule(s). A low molecular weight (<20kD) fraction was able to stimulate T cells from 11 out of 12 donors comprising mainly tuberculoid leprosy patients. The described protocol is well suited to situations where large quantities of antigenic protein mixtures must be processed in order to get the purified molecules/fractions in amounts required for immunoepidemiological studies.

Bacterial Proteins↗
PubMed1999

Differentiation of Lactobacillus isolates from infant faeces by SDS-PAGE and rRNA-targeted oligonucleotide probes.

Isolates of lactobacilli from infant faeces phenotypically characterized as Lactobacillus paracasei subsp. paracasei (six strains), Lact. rhamnosus (six strains), Lact. gasseri (three strains), Lact. acidophilus (one strain) and Lact. fermentum/reuteri (three strains) according to recent classification systems were subjected to SDS-PAGE of whole cell proteins and rRNA-targeted oligonucleotide probe hybridization, in order to confirm the phenotypic characterization and elucidate the exact taxonomic position of the three strains that had properties between fermentum and reuteri. Results suggested a good agreement between the phenotypic characterization, SDS-PAGE and rRNA-targeted oligonucleotide probe hybridization for strains of all species except for the Lact. fermentum/reuteri strains. Results obtained by rRNA probes suggested a possible phylogenetic relatedness of the strains to Lact. reuteri. Isolates from infant faeces with interesting probiotic properties could be used as components of fermented milk products.

Bacterial Proteins↗
PubMed2000

Characterization of hydroxylaminobenzene mutase from pNBZ139 cloned from Pseudomonas pseudoalcaligenes JS45. A highly associated SDS-stable enzyme catalyzing an intramolecular transfer of hydroxy groups.

Hydroxylaminobenzene mutase is the enzyme that converts intermediates formed during initial steps in the degradation of nitrobenzene to a novel ring-fission lower pathway in Pseudomonas pseudoalcaligenes JS45. The mutase catalyzes a rearrangement of hydroxylaminobenzene to 2-aminophenol. The mechanism of the reactions and the properties of the enzymes are unknown. In crude extracts, the hydroxylaminobenzene mutase was stable at SDS concentrations as high as 2%. A procedure including Hitrap-SP, Hitrap-Q and Cu(II)-chelating chromatography was used to partially purify the enzyme from an Escherichia coli clone. The partially purified enzyme was eluted in the void volume of a Superose-12 gel-filtration column even in the presence of 0.05% SDS in 25 mM Tris/HCl buffer, which indicated that it was highly associated. When the enzymatic conversion of hydroxylaminobenzene to 2-aminophenol was carried out in 18O-labeled water, the product did not contain 18O, as determined by GC-MS. The results indicate that the reaction proceeded by intramolecular transfer of the hydroxy group from the nitrogen to the C-2 position of the ring. The mechanism is clearly different from the intermolecular transfer of the hydroxy group in the non-enzymatic Bamberger rearrangement of hydroxylaminobenzene to 4-aminophenol and in the enzymatic hydroxymutation of chorismate to isochorismate.

Aminophenols↗
PubMed2003

SDS-PAGE for identification of species belonging to the Mycobacterium fortuitum complex.

We performed a study to determine the usefulness of SDS-PAGE of whole cell proteins for the characterization of species of rapidly growing mycobacteria belonging to the Mycobacterium fortuitum complex. Strains included 37 M. fortuitum, 32 M. chelonae, 10 M. peregrinum, 5 M. abscessus, and 3 M. mucogenicum. Eight collection strains (including type strains of the five species) were also included in the study. All strains yielded between 44 and 58 bands in the electrophoretograms. Intraspecies similarity showed Dice coefficients higher than 95%, with only one strain of M. fortuitum having a six-band difference (Dice coefficient 87.75%). However, interspecies similarity was always below 75%, the similarity being higher between M. fortuitum and M. peregrinum (75.51%) and between M. chelonae and M. abscessus (54.9%). Visual examination of the electrophoretograms was sufficient for species characterization. SDS-PAGE of whole cell proteins is a useful technique for identification of isolates of the M. fortuitum complex, and is easy to perform without the need for complex or expensive equipment.

Bacterial Proteins↗
PubMed1988

[Changes in the urinary protein pattern in SDS polyacrylamide gel electrophoresis in normal and hypertensive pregnancies].

The urinary protein pattern was determined in 46 healthy male and female subjects, 64 patients with an uncomplicated course of pregnancy and 88 hypertensive pregnant women by use of a special urine preparation and a modified SDS-polyacrylamide gel electrophoresis (SDS-PAGE). There were no differences in the protein electrophoresis pattern between the control subjects, independent of sex and age, and the pregnant women. The number of protein bands did not change in the course of pregnancy and in the post partum period. In both groups, an intensively stained protein band with an apparent molecular weight of 105 kD was detected. In 71 of the 88 hypertensive pregnant women we found a marked reduction in intensity or complete disappearance of the 105 kD protein band. Follow-up analysis in 30 of these pregnant women showed, that in 24 cases disappearance of the 105 kD band occurred simultaneously with and in 6 women before clinical manifestation of the disease. There were no differences in the protein electrophoresis pattern between patients with preexisting renal or hypertensive disease and hypertensive women without a complicated history. In 49 of the 52 hypertensive pregnant women complete reappearance of the 105 kD band was observed 2 to 14 days after delivery. By using silver staining and Western blot, the 105 kD band was identified as Tamm-Horsfall protein. Our findings may reflect a transitory tubular dysfunction in cases of preeclampsia and support the hypothesis of an immunological pathogenesis of the disease.

Adolescent↗
PubMed2000

A simple method of electroelution of individual protein bands from SDS polyacrylamide gels for direct study in cellular assays.

A very simple and effective procedure which allows simultaneous electroelution of separated proteins from SDS polyacrylamide gel into small quantity of elution buffer is described. Elution parameters have been optimized for maximum possible recovery (50-60%). Protein fractions were collected in physiological buffer and an efficient removal of SDS have been obtained, thus fractions collected were suited for direct testing in cell cultures. Method was used to investigate human T-cell responses to purified secreted M tuberculosis H37Rv proteins. Eight low molecular weight (M.w. range 10 kD to 25 kD) culture filtrate proteins were purified in quantities, sufficient for immunological characterization. Lymphocyte proliferative responses and cytokine release pattern from tuberculosis patients, healthy contacts and healthy controls were studied on stimulation with purified culture filtrate proteins. Immunologically important M.tuberculosis proteins were identified by using this method. This approach should be applicable to the rapid identification and characterization of any interesting T cell antigen.

Antigens, Bacterial↗
PubMedDate not supplied

An improved SDS-polyacrylamide gel electrophoresis for resolution of peptides in the range of 3.5-200kDa.

Resolution of a wide range of polypeptides, 3.5-200kDa, on a single low acrylamide and cross linkage gel of 7.7% T, 2.6% C is described here. Laemmli's (4) original discontinuous SDS polyacrylamide gel electrophoresis (SDS-PAGE) system is modified by increasing the ionic strength of both stacking and resolving gels, and replacing the usual glycine buffer with a tricine cathode buffer as described by Schagger and von Jagow (7). This system offers the advantage of a wide range of protein fractionation, with sufficient band resolution, on a single, low acrylamide concentration and cross linkage gel. Moreover, increased gel ionic concentration allows higher protein and salt load, and renders this system suitable for preparative work.

Animals↗
PubMed2001

Isolation of SDS-stable complexes of the intermediate filament protein vimentin with repetitive, mobile, nuclear matrix attachment region, and mitochondrial DNA sequence elements from cultured mouse and human fibroblasts.

Crosslinkage of vimentin to DNA in mouse L929 cells by formaldehyde and isolation of SDS-stable DNA-vimentin complexes from normal L929 cells and mouse and human embryo fibroblasts indicated close spatial relations between these components in the intact cell. The adducts, obtained by immunoprecipitation with anti-vimentin antibody, contained substantial quantities, not only of repetitive and mobile sequence elements such as centromeric satellite DNA, telomere DNA, microsatellites and minisatellites, long and short interspersed nucleotide elements, and retroposons, but also of mitochondrial (mt) DNA. Because the SDS-stable complexes could be isolated with distinctly higher yields from oxidatively stressed, senescent fibroblasts and were dissociated by boiling, they possibly arose from accidental condensation reactions mediated by unsaturated and dialdehydes, products of free radical-induced lipid peroxidation. They can therefore be considered vestiges of a general interaction of vimentin with cellular DNA. The sequence patterns of their DNA fragments were similar to those of extrachromosomal circular and linear DNA, including retroviral elements, markers and enhancers of genomic instability that also occur in the cytoplasm and are able to transport vimentin into the nucleus. Many of the fragments were also remarkably similar to AT-rich nuclear matrix attachment regions (MARs) in that they contained, in addition to various mobile elements, a palette of typical MAR motifs. With its tendency to multimerize and to interact with single-stranded and supercoiled DNA, vimentin thus behaves like a nuclear matrix protein and may as such participate in a variety of nuclear matrix-associated processes such as replication, recombination, repair, and transcription of DNA. These activities seem to be extendible to the mitochondrial compartment, as vimentin was also crosslinked to mtDNA, preferentially to its D-loop and hypervariable main control region. These sites are prone to point and deletion mutations and, like nuclear MARs, are associated with the cyto-karyomatrix. Moreover, as a developmentally regulated and tissue-specific cyto-karyomatrix protein, vimentin may contribute to the organization of chromatin, including centromeric and telomeric heterochromatin at the nuclear periphery, with all its consequences for genomic activities during embryogenesis and in adulthood of vertebrates. However, because of its high affinity for hypervariable, recombinogenic DNA sequences, vimentin is proposed to play a major role in both the preservation and the evolution of the nuclear and mitochondrial genome.

Animals↗