Modification of cysteine residues by alkylation. A tool in peptide mapping and protein identification

Although mass spectrometric peptide mapping has become an established technique for the rapid identification of proteins isolated by polyacrylamide gel electrophoresis (PAGE), the results of the identification procedure can sometimes be ambiguous. Such ambiguities become increasingly prevalent for proteins isolated as mixtures or when only very small amounts of the proteins are isolated. The quality of the identification procedure can be improved by increasing the number of peptides that are extracted from the gel. Here we show that cysteine alkylation is required to ensure maximal coverage in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) peptide mapping of proteins isolated by PAGE. In the described procedure, alkylation was performed prior to electrophoresis to avoid the adventitious formation of acrylamide adducts during electrophoresis. In this way, homogeneous alkylation was obtained with three different alkylating reagents (4-vinylpyridine, iodoacetamide, acrylamide). Cysteine alkylation was also used as a tool for the identification of cysteine-containing peptides. Using a 1:1 mixture of unlabeled acrylamide and deuterium-labeled acrylamide ([2,3,3'-D3]acrylamide), the proteins of interest were alkylated prior to electrophoretic separation. Peptide mixtures produced by trypsin digestion of the resulting protein bands were analyzed by MALDI-TOF MS, and the cysteine content of the peptides was inferred from the isotopic distributions. The cysteine content information was readily obtained and used to improve the protein identification process.     

Gradient polyacrylamide gel electrophoresis in presence of sodium dodecyl sulfate: a practical approach to muscle contractile and regulatory proteins

Two gradient systems for polyacrylamide gel electrophoresis (PAGE) in the presence of sodium dodecyl sulfate (SDS) are described, with emphasis on improvements accumulated over two decades of studies on contractile proteins and regulatory enzymes from smooth muscle. The first "big slab" system utilizes 18 x 20 x 0.1 cm3 gels and a 10-18% acrylamide gradient, optimized for a high resolution of 10 to 500 kDa polypeptides. Eight (or more) gels are cast simultaneously with a gradient formation from "bottom to top" and 20% glycerol is added to the 18% acrylamide solution. The second "minislab" system represents an improved version of the system of Matsudaira and Burgess (Anal. Biochem. 1978, 87, 386-396), with 8 x 10 x 0.05 cm3 gels and 5-15% or 9-18% acrylamide gradient ranges. They are cast from "top to bottom" in 28-piece batches also with the addition of glycerol for improved gradient formation. Both types of gels can also be cast individually using a specially designed pestle-type gradient maker. For gel destaining, a convenient continuous hydrodynamic destainer is also described.     

Fourier transform Raman spectroscopy of polyacrylamide gels (PAGs) for radiation dosimetry

Polyacrylamide gels (PAGs) are used for magnetic resonance imaging radiation dosimetry. Fourier transform (FT) Raman spectroscopy studies were undertaken to investigate cross-linking changes during the copolymerization of polyacrylamide gels in the spectral range of 200-3500 cm(-1). Vibrational bands of 1285 cm(-1) and 1256 cm(-1) were assigned to acrylamide and bis-acrylamide single CH2 deltaCH2 binding modes. Bands were found to decrease in amplitude with increasing absorbed radiation dose as a result of copolymerization. Principal component regression was performed on FT-Raman spectra of PAG samples irradiated to 50 Gy. Two components were found to be sufficient to account for 98.7% of the variance in the data. Cross validation was used to establish the absorbed radiation dose of an unknown PAG sample from the FT-Raman spectra. The calculated correlation coefficient between measured and predictive samples was 0.997 with a standard error of estimate of 0.976 and a standard error of prediction of 1.140. Results demonstrate the potential of FT-Raman spectroscopy for ionizing radiation dosimetry using polyacrylamide gels.     

Cyclic changes in platelet dynamics and the pathogenesis and prophylaxis of migraine

Continuous linear gradients improve electrophoretic separations in polyacrylamide. They are obtained by overlayering equal volumes of two monomer solutions with different acrylamide concentrations, namely 180-260 and 23-50 g/l, in the usual gel tubes. The tubes are tilted 3-10 degrees to the horizontal, and rotated around their longitudinal axis until the parts of both solutions in contact are mixed homogeneously. Subsequent polymerization takes place in the vertical position. The more concentrated lower solution contains 4-nitrophenol, so that the final polymer concentration at any point of the gel can be measured densitometrically. The construction and handling of the rotation device are simple and yield highly reproducible results. This versatile method was evaluated for the separation of proteins, lipoproteins, and enzymes in human serum and yields 27-30 protein fractions by additional use of a pH-gradient.     

Preparative isoelectric focusing in multicompartment electrolyzers: novel, hydrolytically stable and hydrophilic isoelectric membranes

Preparative isoelectric focusing in multicompartment electrolyzers is based on the production of isoelectric membranes of precise isoelectric point, able to buffer at their pI value and to titrate proteins tangent to or crossing the membranes. Up to the present, such membranes have been based on polyacrylamide chemistry; acrylamide, however, is neither stable in acidic nor basic environments. We describe here novel membranes, produced with a unique monomer, N-acryloylaminoethoxyethanol (AAEE). Poly(AAEE) membranes are extremely stable to alkaline hydrolysis (500 times more stable than polyacrylamide) and even more hydrophilic than the latter matrix. This allows production of highly reproducible membranes (these do not change their pI with time, since no acrylic acid is produced by hydrolysis upon storage) which do not adsorb proteins by hydrophobic interaction.     

Immunoglobulin E, viral antibodies and obstructive lung disease in adults. The relation between antibody level in serum, lung function and non-specific bronchial reactivity

The electrophoretic mobilities of DNA molecules in three different molecular weight ladders were measured in polyacrylamide gels containing different acrylamide concentrations (%T) and cross-linker ratios (%C), cast and run in Trisacetate-EDTA (TAE) buffer. The apparent pore radius of each gel was estimated from Ferguson plots of the relative mobilities of each of the DNA molecules, using the mobility of the monomer fragment in each molecular weight ladder as the reference mobility. The effective size of each of the DNA molecules was estimated from its radius of gyration. The apparent gel pore radii calculated in this manner ranged from 21 nm in gels containing 10.5%T, 5%C to 200 nm in gels with 4.6%T, 2%C, similar to the values observed for polyacrylamide gels cast and run in Tris-borate-EDTA (TBE) buffer (Holmes and Stellwagen, Electrophoresis 1991, 12, 612-619). Hence, the effective pore size of polyacrylamide gels is essentially independent of whether the gels are cast and run in TAE or TBE buffer.     

Comparative acute toxicity and primary irritancy of the ethylidene and vinyl isomers of norbornene

Perlecan and aggrecan are proteoglycans that receive primarily heparan sulfate and chondroitin sulfate side chains, respectively. Their large multidomained core proteins have little or no homology to each other and their glycosaminoglycan (GAG) attachment sites are restricted to certain domains only. We examined the involvement of the non-GAG bearing domains in designating the GAG type added to the GAG attachment domain by preparing cDNA constructs that expressed perlecan/aggrecan chimeras as recombinant products in COS-7 cells and then determining the size and GAG composition of the recombinant products. The results showed that domain I of perlecan receives primarily (73-81%) heparan sulfate when coupled with domain II and III of perlecan, but when coupled with the G3 domain of aggrecan, it receives primarily (59-63%) chondroitin sulfate. Furthermore, the chondroitin sulfate attachment region of aggrecan received GAG side chains more readily when coupled to the G3 domain of aggrecan than when coupled to domains II and III of perlecan. The GAG side chains on all these recombinant products were small and similar in size. These findings indicate that the utilization of attachment sites for heparan and chondroitin sulfate or the sulfation of these GAGs can be influenced, in part, by non-GAG bearing domains.     

Effect of protein application mode and acrylamide concentration on the resolution of protein spots separated by two-dimensional gel electrophoresis

Two-dimensional gel electrophoresis separates large numbers of proteins in two steps on the basis of differences in their pIs and molecular masses. The separation is usually performed on immobilized pH gradient strips, followed by gradient polyacrylamide gels separating proteins with molecular masses between 5-200 kDa. For the first-dimensional separation the protein samples are usually applied near one end of the strip. Using total soluble protein extracts of the bacterium Haemophilus influenzae, we found that simultaneous sample application at both the basic and the acidic ends of the strip resulted in detection of more and stronger protein spots in comparison with sample application at one end only. Because many proteins of an organism have similar pI and Mr values, an overlapping of protein spots is frequently observed in the second-dimensional separation. The soluble protein fraction of H. influenzae was further separated on gels of constant acrylamide concentration between 7.5% and 15.0%. We found that for proteins of molecular mass within certain ranges, the gels of homogeneous acrylamide concentration provided more efficient spot separation than the gradient gels. The observed improvements in spot resolution may be useful in the characterization of proteins from other organisms or cell lines.     

Polyacrylamide-based glycoconjugates as tools in glycobiology

This review describes the synthesis, physicochemical characteristics and application for studying carbohydrate-binding proteins of polyacrylamide (PAA) type neoglycoconjugates. An approach to the synthesis of conjugates based on the interaction of activated polyacrylic acid with omega-aminoalkyl glycosides has been developed. Both the molecules of Glyc-PAA and the conjugates bearing various labels and effectors, as well as sorbents, and glycosurfaces can be designed using this method. Examples of the application of the conjugates as tools for the study of lectins, antibodies, and glycosyltransferases in glycobiology, cytochemistry and histochemistry are described along with the prospects of the further development of the presented approach in glycotechnology and medicine.     

Molecular weights of three mouse milk caseins by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and kappa-like characteristics of a fourth casein

Caseins of mouse milk are phosphoproteins which precipitate at pH 4.6, stain blue with "Stains-all," and stain red with "Stains-all" following alkaline phosphatase digestion. Four caseins were separated electrophoretically in sodium dodecyl sulfate-polyacrylamide gels varying from 8.5 to 15% acrylamide. Molecular weights for three of these proteins were 43,200, 27,700, and 25,900. The molecular weights determined for bovine alphas1 and beta caseins by this method were similar to those previously obtained by other methods. A fourth mouse casein contained carbohydrate, phosphorus, and sialic acid. This protein was rennin-sensitive and behaved anomalously on sodium dodecyl sulfate polyacrylamide gels, as did bovine kappa-casein. Because of similarities with bovine kappa-casein, it was designated with "kappa-casein" of mouse milk.     

Multiple heparan sulfate chains are required for optimal syndecan-1 function

Syndecans have three highly conserved sites available for heparan sulfate attachment. To determine if all three sites are required for normal function, a series of mutated syndecans having two, one, or no heparan sulfate chains were expressed in ARH-77 cells. Previously, we demonstrated that expression of wild-type syndecan-1 on these myeloma cells mediates cell-matrix and cell-cell adhesion and inhibits cell invasion into collagen gels. Here we show that to optimally mediate each of these activities, all three sites of heparan sulfate attachment are required. Generally, an increasing loss of syndecan-1 function occurs as the number of heparan sulfate attachment sites decreases. This loss of function is not the result of a decrease in either the total amount of cell surface heparan sulfate or syndecan-1 core protein. In regard to cell invasion, cells expressing syndecan-1 bearing a single heparan sulfate attachment site exhibit a hierarchy of function based upon the position of the site within the core protein; the presence of an available attachment site at serine 47 confers the greatest level of activity, while serine 37 contributes little to syndecan-1 function. However, when all three heparan sulfate chains are present, significantly greater biological activity is observed than is predicted by the sum of the activities occurring when the chains act individually. This synergy provides a functional basis for the evolutionary conservation of the three heparan sulfate attachment sites on syndecans and supports the idea that molecular heterogeneity, which is characteristic of proteoglycans, contributes to their functional diversity.     

聚丙烯酰胺对铝土矿浮选尾矿沉降性能的影响

不同离子类型、分子量及用量的聚丙烯酰胺对尾矿沉降性能的影响表明,阴离子型聚丙烯酰胺的效果好于阳离子和非离子型。调节矿浆pH=7以下,加入阴离子聚丙烯酰胺就能实现尾矿的较快沉降,分子量为1 400万的阴离子型聚丙烯酰胺能取得最佳的沉降效果。经聚丙烯酰胺处理后的尾矿水能回用至浮选流程中,低含量的聚丙烯酰胺能改善铝土矿的浮选指标。     

Attachment theory and research and the psychoanalytic process.

Attachment theory, along with relevant research, is reviewed in terms of its usefulness as a developmental theory for conceptualizing aspects of the psychoanalytic process. Because of its emphasis on the development of relationships through the process of dyadic interaction, attachment theory offers an alternative conceptualization for understanding the relationship aspects of the clinical psychoanalytic process. Manifestations of early attachment behavior can be understood as being recreated in the course of psychoanalysis and can contribute to a developmental understanding of the process. Because many psychiatric problems can be attributed to difficulties in the development of an attachment relationship, it is also possible that attachment theory may be helpful in providing further understanding of the etiology of deviations in development. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

SDS agarose gels for analysis of proteins

A new agarose-based protein electrophoresis gel system is described. The system consists of a highly resolving agarose, MetaPhor XR (FMC BioProducts, Rockland, ME, USA) dissolved in urea and TBE buffer and a stacking gel composed of a high gel-strength agarose, SeaKem Gold (FMC BioProducts). TBE containing sodium dodecyl sulfate (SDS) is used as electrophoresis buffer. The disadvantages of traditional agarose gels have been overcome, and several advantages over polyacrylamide gels have been demonstrated. The system is capable of high-resolution separation of small proteins and has a dynamic separation range equivalent to a 4%-20% gradient polyacrylamide gel. Furthermore, the staining of protein bands by Coomassie Brilliant Blue is very uniform in this gel, and depending on the protein, higher detection sensitivity can be obtained compared to SDS polyacrylamide gels. In Western blotting, proteins are more efficiently transferred to the membrane from the agarose gel than from polyacrylamide gels. Finally, the exceptional stability of agarose allows for gels to be precast and stored for a year.     

Development of a highly polymorphic STR marker for identity testing purposes at the human androgen receptor gene (HUMARA)

We developed a non-isotopic method which improves the technical quality of the X-linked HUMARA locus typing process. The use of formamide and a low concentration of acrylamide increased resolution and sharpness of HUMARA alleles in silver-stained polyacrylamide gels. In addition, the construction of an allelic ladder containing amplified sequence of 9 alleles (even-numbered alleles) of the HUMARA locus, allows confident, rapid and precise assignment of discretely defined alleles. Allele and genotype frequencies for the HUMARA locus were determined in a French Canadian population sample. Observed genotype frequencies in females conformed to Hardy-Weinberg expectations. Furthermore, the HUMARA locus is highly polymorphic with 18 observed alleles and an heterozygosity value of 89.3%. Also, this locus has average powers of discrimination of 97.8% and 88.7% for testing samples of female and male origin, respectively. In the French Canadian population, the average probability of excluding a random man as the father in paternity analysis when both mother and daughter are tested for this locus is 88.0%. Together, the results indicate that the HUMARA locus provides a highly discriminatory system that is appropriate for the purposes of forensic identification and paternity testing involving a female child.     

Acrylamide induces immediate-early gene expression in rat brain

Northern blot analysis was used to study the effects of acrylamide, a potent neurotoxin, on the induction of c-fos and c-jun mRNA in rat brain. Male Sprague-Dawley rats (10-12 weeks old) treated with acrylamide as a single dose (100 mg/kg, i.p.) or via drinking water (0.03% w/v) for 4 weeks, were used to study acute and chronic effects on immediate-early gene expression, respectively. Acute administration of acrylamide caused a statistically significant increase in the expression of c-fos (approx. 37%) and c-jun (approx. 17%) mRNA in rat brain. By contrast, the level of c-fos mRNA in chronic acrylamide treatment was not altered significantly, but the expression of c-jun mRNA was increased almost 100% as compared to control. These data show that the neurotoxin acrylamide induces immediate-early gene expression in the brain. The effects appear to be related to the route of administration, dose and duration of acrylamide treatment.     

The resolution between two native proteins and between their sodium dodecyl sulfate-complexes in agarose and polyacrylamide gel electrophoresis

Commercial gel electrophoresis apparatus with intermittent fluorescence scanning of the migration path (HPGE-1000 apparatus, LabIntelligence) makes it possible to measure band width and migration distance as a function of the duration of electrophoresis. As a result, resolution can be evaluated quantitatively and therefore different gel media can be compared objectively. The resolution of fluorescein carboxylate labeled conalbumin (molecular mass 86 kDa) and soybean trypsin inhibitor (22.7 kDa) in gel electrophoresis was found to increase as a function of the gel type in the order SeaKem GTG-, SeaKem Gold-agarose, 2% N,N'-methylenebisacrylamide cross-linked polyacrylamide, MetaPhor-XR-, and SeaPrep-agarose. The advantage in resolving capacity of SeaPrep agarose over the polyacrylamide gel was by a factor of up to five. The resolving capacity of the agaroses was in indirect relation to the degree of electroendosmosis. In all media, resolution increased with migration distance (time). The same proteins when reacted with sodium dodecyl sulfate (SDS) resolve (i) better at up to 6% SeaPrep agarose concentration than in polyacrylamide, as in the gel electrophoresis of the native proteins; (ii) less effectively, by contrast, at SeaPrep agarose concentrations > 6%, than in polyacrylamide gel; and (iii) significantly better in 4-6% SeaPrep agarose than in 4-6% SeaKem GTG agarose. Since Ferguson plot analysis in both agarose and polyacrylamide gels shows that the two SDS-proteins are larger than the native proteins with which they are complexed, the superiority of polyacrylamide gels above 7% appears to be correlated with the fact that its mean pore radius, estimated for both media using identical assumptions and identical rigid spherical standards - proteins, is approximately seven times larger than that of SeaPrep agarose in the concentration range of 3-8%, and that therefore the molecular "fit" in polyacrylamide is closer than that in SeaPrep agarose of the concentration range used. The dependence of resolution on the ratio of particle radius to mean pore radius ("fit") is also suggested by the fact that the two SDS-proteins resolve in a biphasic dependence on gel concentration in both agarose and polyacrylamide, with a maximum at 6% agarose and 10% polyacrylamide.     

Synthesis and properties of acrylamide-substituted base pair specific dyes for deoxyribonucleic acid template mediated synthesis of dye polymers

We have tried to construct synthetic polymers for sequence-specific recognition and complexation of longer deoxynucleotide sequences. For this purpose, we developed a method of template-directed polymerization of basic pair specific DNA ligands such as basic dyes. The template-directed polymerization consists in a copolymerization of various dyes of different specificities staying simultaneously in a binding equilibrium with DNA. In the present paper, we describe the synthesis and the properties of base pair specific monomers especially designed for performance of radical chain polymerization reactions in aqueous medium at room temperature. Different acrylamide derivatives of well-known dyes, such as AT-specific malachite green and GC-specific phenyl neutral red, were synthesized and studied for their ability of base pair specific complex formation with DNA of different base composition. Partition equilibrium dialysis and dye titration agarose gel electrophoresis were used to ensure for several dyes that they may be incorporated into different polymers via copolymerization of their acrylamido derivatives with various small base-unspecific monomers without substantial change of their binding parameters. Furthermore, we demonstrate that acrylamide and other small acrylamide derivatives can be used as building blocks for the synthesis of polymeric links between base pair specific monomers. The results and their consequences for template polymerization reactions are discussed.     

History, race, and attachment to place among elders in the rural all-black towns of Oklahoma

This research examines place attachment among older residents of the all-Black towns of Oklahoma. Social-historical occurrences, personal experiences associated with race, and expressed differences between social-historical groupings of older African Americans influence the level of social and autobiographical insideness among the elderly residents. The findings extend current conceptualizations of place attachment by showing that (a) place attachment is not a constant, even among long-term residents; (b) social-historical factors can play an important role in the level of place attachment; (c) race can be a salient element of place attachment; (d) experiences outside the community, such as racial discrimination, can influence the level of social and autobiographical bonding to the community; and (e) subgroup identity within minority groups can be associated with variations in community place attachment. The findings point to the value of carefully examining the issues of history and race in research focusing on older minority group members.     

Attending to the exploration side of infant attachment: Contributions from self-determination theory.

Understanding the intergenerational transmission of attachment patterns has been a main focus of attachment research for many years. Most of the empirical work conducted on this question has addressed maternal sensitivity to infants’ attachment needs. Given that security of attachment is defined as an attachment/exploration balance, some researchers have stressed the need to explore maternal behaviours in the context of infant exploration. The authors propose that self-determination theory (SDT) could contribute to attachment work in this respect given that it has clearly operationalized parental exploration-related behaviours and has related them to numerous child outcomes. This article highlights conceptual, empirical, and methodological parallels that can be drawn between SDT and attachment theory, thus suggesting that they could be complementary on many levels. (PsycINFO Database Record (c) 2010 APA, all rights reserved)